From fc5f8d8c2dffb24b79ef7450172d50f8725f6efb Mon Sep 17 00:00:00 2001 From: Adam Egger Date: Tue, 3 Nov 2020 11:38:14 -0800 Subject: [PATCH 01/23] start to add calibration arp script --- jet_tracking/__init__.py | 10 - .../jet_tracking_cal/jet_tracking_cal.ipynb | 25803 ++++++++++++++++ jet_tracking/jet_tracking_cal/jt_cal.py | 410 + jet_tracking/jet_tracking_cal/jt_cal_arp.py | 17 + .../jet_tracking_cal/submit_jt_arp.sh | 5 + 5 files changed, 26235 insertions(+), 10 deletions(-) create mode 100644 jet_tracking/jet_tracking_cal/jet_tracking_cal.ipynb create mode 100644 jet_tracking/jet_tracking_cal/jt_cal.py create mode 100644 jet_tracking/jet_tracking_cal/jt_cal_arp.py create mode 100644 jet_tracking/jet_tracking_cal/submit_jt_arp.sh diff --git a/jet_tracking/__init__.py b/jet_tracking/__init__.py index 6853e21..e69de29 100644 --- a/jet_tracking/__init__.py +++ b/jet_tracking/__init__.py @@ -1,10 +0,0 @@ -from . import cam_utils # noqa -from . import devices # noqa -from . import jet_control # noqa -from ._version import get_versions - -try: - __version__ = get_versions()['version'] - del get_versions -except Exception: - __version__ = '0.0.0-unknown' diff --git a/jet_tracking/jet_tracking_cal/jet_tracking_cal.ipynb b/jet_tracking/jet_tracking_cal/jet_tracking_cal.ipynb new file mode 100644 index 0000000..3851b40 --- /dev/null +++ b/jet_tracking/jet_tracking_cal/jet_tracking_cal.ipynb @@ -0,0 +1,25803 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "
\n", + " \n", + " Loading BokehJS ...\n", + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/javascript": [ + "\n", + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " var force = true;\n", + "\n", + " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", + " root._bokeh_onload_callbacks = [];\n", + " root._bokeh_is_loading = undefined;\n", + " }\n", + "\n", + " var JS_MIME_TYPE = 'application/javascript';\n", + " var HTML_MIME_TYPE = 'text/html';\n", + " var EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", + " var CLASS_NAME = 'output_bokeh rendered_html';\n", + "\n", + " /**\n", + " * Render data to the DOM node\n", + " */\n", + " function render(props, node) {\n", + " var script = document.createElement(\"script\");\n", + " node.appendChild(script);\n", + " }\n", + "\n", + " /**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + " function handleClearOutput(event, handle) {\n", + " var cell = handle.cell;\n", + "\n", + " var id = cell.output_area._bokeh_element_id;\n", + " var server_id = cell.output_area._bokeh_server_id;\n", + " // Clean up Bokeh references\n", + " if (id != null && id in Bokeh.index) {\n", + " Bokeh.index[id].model.document.clear();\n", + " delete Bokeh.index[id];\n", + " }\n", + "\n", + " if (server_id !== undefined) {\n", + " // Clean up Bokeh references\n", + " var cmd = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", + " cell.notebook.kernel.execute(cmd, {\n", + " iopub: {\n", + " output: function(msg) {\n", + " var id = msg.content.text.trim();\n", + " if (id in Bokeh.index) {\n", + " Bokeh.index[id].model.document.clear();\n", + " delete Bokeh.index[id];\n", + " }\n", + " }\n", + " }\n", + " });\n", + " // Destroy server and session\n", + " var cmd = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", + " cell.notebook.kernel.execute(cmd);\n", + " }\n", + " }\n", + "\n", + " /**\n", + " * Handle when a new output is added\n", + " */\n", + " function handleAddOutput(event, handle) {\n", + " var output_area = handle.output_area;\n", + " var output = handle.output;\n", + "\n", + " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", + " if ((output.output_type != \"display_data\") || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n", + " return\n", + " }\n", + "\n", + " var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + "\n", + " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", + " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", + " // store reference to embed id on output_area\n", + " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " }\n", + " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", + " var bk_div = document.createElement(\"div\");\n", + " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", + " var script_attrs = bk_div.children[0].attributes;\n", + " for (var i = 0; i < script_attrs.length; i++) {\n", + " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", + " }\n", + " // store reference to server id on output_area\n", + " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", + " }\n", + " }\n", + "\n", + " function register_renderer(events, OutputArea) {\n", + "\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " var toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[toinsert.length - 1]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " /* Handle when an output is cleared or removed */\n", + " events.on('clear_output.CodeCell', handleClearOutput);\n", + " events.on('delete.Cell', handleClearOutput);\n", + "\n", + " /* Handle when a new output is added */\n", + " events.on('output_added.OutputArea', handleAddOutput);\n", + "\n", + " /**\n", + " * Register the mime type and append_mime function with output_area\n", + " */\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " /* Is output safe? */\n", + " safe: true,\n", + " /* Index of renderer in `output_area.display_order` */\n", + " index: 0\n", + " });\n", + " }\n", + "\n", + " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", + " if (root.Jupyter !== undefined) {\n", + " var events = require('base/js/events');\n", + " var OutputArea = require('notebook/js/outputarea').OutputArea;\n", + "\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " }\n", + "\n", + " \n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " var NB_LOAD_WARNING = {'data': {'text/html':\n", + " \"
\\n\"+\n", + " \"

\\n\"+\n", + " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", + " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", + " \"

\\n\"+\n", + " \"\\n\"+\n", + " \"\\n\"+\n", + " \"from bokeh.resources import INLINE\\n\"+\n", + " \"output_notebook(resources=INLINE)\\n\"+\n", + " \"\\n\"+\n", + " \"
\"}};\n", + "\n", + " function display_loaded() {\n", + " var el = document.getElementById(\"1001\");\n", + " if (el != null) {\n", + " el.textContent = \"BokehJS is loading...\";\n", + " }\n", + " if (root.Bokeh !== undefined) {\n", + " if (el != null) {\n", + " el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n", + " }\n", + " } else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(display_loaded, 100)\n", + " }\n", + " }\n", + "\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " root._bokeh_onload_callbacks.forEach(function(callback) {\n", + " if (callback != null)\n", + " callback();\n", + " });\n", + " } finally {\n", + " delete root._bokeh_onload_callbacks\n", + " }\n", + " console.debug(\"Bokeh: all callbacks have finished\");\n", + " }\n", + "\n", + " function load_libs(css_urls, js_urls, callback) {\n", + " if (css_urls == null) css_urls = [];\n", + " if (js_urls == null) js_urls = [];\n", + "\n", + " root._bokeh_onload_callbacks.push(callback);\n", + " if (root._bokeh_is_loading > 0) {\n", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls == null || js_urls.length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + "\n", + " function on_error() {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " for (var i = 0; i < css_urls.length; i++) {\n", + " var url = css_urls[i];\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error;\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " for (var i = 0; i < js_urls.length; i++) {\n", + " var url = js_urls[i];\n", + " var element = document.createElement('script');\n", + " element.onload = on_load;\n", + " element.onerror = on_error;\n", + " element.async = false;\n", + " element.src = url;\n", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " };var element = document.getElementById(\"1001\");\n", + " if (element == null) {\n", + " console.error(\"Bokeh: ERROR: autoload.js configured with elementid '1001' but no matching script tag was found. \")\n", + " return false;\n", + " }\n", + "\n", + " function inject_raw_css(css) {\n", + " const element = document.createElement(\"style\");\n", + " element.appendChild(document.createTextNode(css));\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " \n", + " var js_urls = [\"https://cdn.pydata.org/bokeh/release/bokeh-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-tables-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-gl-1.4.0.min.js\"];\n", + " var css_urls = [];\n", + " \n", + "\n", + " var inline_js = [\n", + " function(Bokeh) {\n", + " inject_raw_css(\".widget-box {\\n\\tmin-height: 20px;\\n\\tbackground-color: #f5f5f5;\\n\\tborder: 1px solid #e3e3e3 !important;\\n\\tborder-radius: 4px;\\n\\t-webkit-box-shadow: inset 0 1px 1px rgba(0,0,0,.05);\\n\\tbox-shadow: inset 0 1px 1px rgba(0,0,0,.05);\\n\\toverflow-x: hidden;\\n\\toverflow-y: hidden;\\n}\\n\\n.scrollable {\\n overflow: scroll;\\n}\\n\\nprogress {\\n\\tappearance: none;\\n\\t-moz-appearance: none;\\n\\t-webkit-appearance: none;\\n\\n\\tborder: none;\\n\\theight: 20px;\\n\\tbackground-color: whiteSmoke;\\n\\tborder-radius: 3px;\\n\\tbox-shadow: 0 2px 3px rgba(0,0,0,.5) inset;\\n\\tcolor: royalblue;\\n\\tposition: relative;\\n\\tmargin: 0 0 1.5em;\\n}\\n\\nprogress[value]::-webkit-progress-bar {\\n\\tbackground-color: whiteSmoke;\\n\\tborder-radius: 3px;\\n\\tbox-shadow: 0 2px 3px rgba(0,0,0,.5) inset;\\n}\\n\\nprogress[value]::-webkit-progress-value {\\n\\tposition: relative;\\n\\n\\tbackground-size: 35px 20px, 100% 100%, 100% 100%;\\n\\tborder-radius:3px;\\n}\\n\\nprogress.active:not([value])::before {\\n\\tbackground-position: 10%;\\n\\tanimation-name: stripes;\\n\\tanimation-duration: 3s;\\n\\tanimation-timing-function: linear;\\n\\tanimation-iteration-count: infinite;\\n}\\n\\nprogress[value]::-moz-progress-bar {\\n\\tbackground-size: 35px 20px, 100% 100%, 100% 100%;\\n\\tborder-radius:3px;\\n}\\n\\nprogress:not([value])::-moz-progress-bar {\\n\\tborder-radius:3px;\\n\\tbackground:\\n\\tlinear-gradient(-45deg, transparent 33%, rgba(0, 0, 0, 0.2) 33%, rgba(0, 0, 0, 0.2) 66%, transparent 66%) left/2.5em 1.5em;\\n\\n}\\n\\nprogress.active:not([value])::-moz-progress-bar {\\n\\tbackground-position: 10%;\\n\\tanimation-name: stripes;\\n\\tanimation-duration: 3s;\\n\\tanimation-timing-function: linear;\\n\\tanimation-iteration-count: infinite;\\n}\\n\\nprogress.active:not([value])::-webkit-progress-bar {\\n\\tbackground-position: 10%;\\n\\tanimation-name: stripes;\\n\\tanimation-duration: 3s;\\n\\tanimation-timing-function: linear;\\n\\tanimation-iteration-count: infinite;\\n}\\n\\nprogress.primary[value]::-webkit-progress-value { background-color: #007bff; }\\nprogress.primary:not([value])::before { background-color: #007bff; }\\nprogress.primary:not([value])::-webkit-progress-bar { background-color: #007bff; }\\nprogress.primary::-moz-progress-bar { background-color: #007bff; }\\n\\nprogress.secondary[value]::-webkit-progress-value { background-color: #6c757d; }\\nprogress.secondary:not([value])::before { background-color: #6c757d; }\\nprogress.secondary:not([value])::-webkit-progress-bar { background-color: #6c757d; }\\nprogress.secondary::-moz-progress-bar { background-color: #6c757d; }\\n\\nprogress.success[value]::-webkit-progress-value { background-color: #28a745; }\\nprogress.success:not([value])::before { background-color: #28a745; }\\nprogress.success:not([value])::-webkit-progress-bar { background-color: #28a745; }\\nprogress.success::-moz-progress-bar { background-color: #28a745; }\\n\\nprogress.danger[value]::-webkit-progress-value { background-color: #dc3545; }\\nprogress.danger:not([value])::before { background-color: #dc3545; }\\nprogress.danger:not([value])::-webkit-progress-bar { background-color: #dc3545; }\\nprogress.danger::-moz-progress-bar { background-color: #dc3545; }\\n\\nprogress.warning[value]::-webkit-progress-value { background-color: #ffc107; }\\nprogress.warning:not([value])::before { background-color: #ffc107; }\\nprogress.warning:not([value])::-webkit-progress-bar { background-color: #ffc107; }\\nprogress.warning::-moz-progress-bar { background-color: #ffc107; }\\n\\nprogress.info[value]::-webkit-progress-value { background-color: #17a2b8; }\\nprogress.info:not([value])::before { background-color: #17a2b8; }\\nprogress.info:not([value])::-webkit-progress-bar { background-color: #17a2b8; }\\nprogress.info::-moz-progress-bar { background-color: #17a2b8; }\\n\\nprogress.light[value]::-webkit-progress-value { background-color: #f8f9fa; }\\nprogress.light:not([value])::before { background-color: #f8f9fa; }\\nprogress.light:not([value])::-webkit-progress-bar { background-color: #f8f9fa; }\\nprogress.light::-moz-progress-bar { background-color: #f8f9fa; }\\n\\nprogress.dark[value]::-webkit-progress-value { background-color: #343a40; }\\nprogress.dark:not([value])::-webkit-progress-bar { background-color: #343a40; }\\nprogress.dark:not([value])::before { background-color: #343a40; }\\nprogress.dark::-moz-progress-bar { background-color: #343a40; }\\n\\nprogress:not([value])::-webkit-progress-bar {\\n\\tborder-radius: 3px;\\n\\tbackground:\\n\\tlinear-gradient(-45deg, transparent 33%, rgba(0, 0, 0, 0.2) 33%, rgba(0, 0, 0, 0.2) 66%, transparent 66%) left/2.5em 1.5em;\\n}\\nprogress:not([value])::before {\\n\\tcontent:\\\" \\\";\\n\\tposition:absolute;\\n\\theight: 20px;\\n\\ttop:0;\\n\\tleft:0;\\n\\tright:0;\\n\\tbottom:0;\\n\\tborder-radius: 3px;\\n\\tbackground:\\n\\tlinear-gradient(-45deg, transparent 33%, rgba(0, 0, 0, 0.2) 33%, rgba(0, 0, 0, 0.2) 66%, transparent 66%) left/2.5em 1.5em;\\n}\\n\\n@keyframes stripes {\\n from {background-position: 0%}\\n to {background-position: 100%}\\n}\");\n", + " },\n", + " function(Bokeh) {\n", + " inject_raw_css(\".json-formatter-row {\\n font-family: monospace;\\n}\\n.json-formatter-row,\\n.json-formatter-row a,\\n.json-formatter-row a:hover {\\n color: black;\\n text-decoration: none;\\n}\\n.json-formatter-row .json-formatter-row {\\n margin-left: 1rem;\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty {\\n opacity: 0.5;\\n margin-left: 1rem;\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty:after {\\n display: none;\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-object:after {\\n content: \\\"No properties\\\";\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-array:after {\\n content: \\\"[]\\\";\\n}\\n.json-formatter-row .json-formatter-string,\\n.json-formatter-row .json-formatter-stringifiable {\\n color: green;\\n white-space: pre;\\n word-wrap: break-word;\\n}\\n.json-formatter-row .json-formatter-number {\\n color: blue;\\n}\\n.json-formatter-row .json-formatter-boolean {\\n color: red;\\n}\\n.json-formatter-row .json-formatter-null {\\n color: #855A00;\\n}\\n.json-formatter-row .json-formatter-undefined {\\n color: #ca0b69;\\n}\\n.json-formatter-row .json-formatter-function {\\n color: #FF20ED;\\n}\\n.json-formatter-row .json-formatter-date {\\n background-color: rgba(0, 0, 0, 0.05);\\n}\\n.json-formatter-row .json-formatter-url {\\n text-decoration: underline;\\n color: blue;\\n cursor: pointer;\\n}\\n.json-formatter-row .json-formatter-bracket {\\n color: blue;\\n}\\n.json-formatter-row .json-formatter-key {\\n color: #00008B;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-row .json-formatter-toggler-link {\\n cursor: pointer;\\n}\\n.json-formatter-row .json-formatter-toggler {\\n line-height: 1.2rem;\\n font-size: 0.7rem;\\n vertical-align: middle;\\n opacity: 0.6;\\n cursor: pointer;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-row .json-formatter-toggler:after {\\n display: inline-block;\\n transition: transform 100ms ease-in;\\n content: \\\"\\\\25BA\\\";\\n}\\n.json-formatter-row > a > .json-formatter-preview-text {\\n opacity: 0;\\n transition: opacity 0.15s ease-in;\\n font-style: italic;\\n}\\n.json-formatter-row:hover > a > .json-formatter-preview-text {\\n opacity: 0.6;\\n}\\n.json-formatter-row.json-formatter-open > .json-formatter-toggler-link .json-formatter-toggler:after {\\n transform: rotate(90deg);\\n}\\n.json-formatter-row.json-formatter-open > .json-formatter-children:after {\\n display: inline-block;\\n}\\n.json-formatter-row.json-formatter-open > a > .json-formatter-preview-text {\\n display: none;\\n}\\n.json-formatter-row.json-formatter-open.json-formatter-empty:after {\\n display: block;\\n}\\n.json-formatter-dark.json-formatter-row {\\n font-family: monospace;\\n}\\n.json-formatter-dark.json-formatter-row,\\n.json-formatter-dark.json-formatter-row a,\\n.json-formatter-dark.json-formatter-row a:hover {\\n color: white;\\n text-decoration: none;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-row {\\n margin-left: 1rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty {\\n opacity: 0.5;\\n margin-left: 1rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty:after {\\n display: none;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-object:after {\\n content: \\\"No properties\\\";\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-array:after {\\n content: \\\"[]\\\";\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-string,\\n.json-formatter-dark.json-formatter-row .json-formatter-stringifiable {\\n color: #31F031;\\n white-space: pre;\\n word-wrap: break-word;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-number {\\n color: #66C2FF;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-boolean {\\n color: #EC4242;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-null {\\n color: #EEC97D;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-undefined {\\n color: #ef8fbe;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-function {\\n color: #FD48CB;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-date {\\n background-color: rgba(255, 255, 255, 0.05);\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-url {\\n text-decoration: underline;\\n color: #027BFF;\\n cursor: pointer;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-bracket {\\n color: #9494FF;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-key {\\n color: #23A0DB;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler-link {\\n cursor: pointer;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler {\\n line-height: 1.2rem;\\n font-size: 0.7rem;\\n vertical-align: middle;\\n opacity: 0.6;\\n cursor: pointer;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler:after {\\n display: inline-block;\\n transition: transform 100ms ease-in;\\n content: \\\"\\\\25BA\\\";\\n}\\n.json-formatter-dark.json-formatter-row > a > .json-formatter-preview-text {\\n opacity: 0;\\n transition: opacity 0.15s ease-in;\\n font-style: italic;\\n}\\n.json-formatter-dark.json-formatter-row:hover > a > .json-formatter-preview-text {\\n opacity: 0.6;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > .json-formatter-toggler-link .json-formatter-toggler:after {\\n transform: rotate(90deg);\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > .json-formatter-children:after {\\n display: inline-block;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > a > .json-formatter-preview-text {\\n display: none;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open.json-formatter-empty:after {\\n display: block;\\n}\\n\");\n", + " },\n", + " function(Bokeh) {\n", + " inject_raw_css(\".codehilite .hll { background-color: #ffffcc }\\n.codehilite { background: #f8f8f8; }\\n.codehilite .c { color: #408080; font-style: italic } /* Comment */\\n.codehilite .err { border: 1px solid #FF0000 } /* Error */\\n.codehilite .k { color: #008000; font-weight: bold } /* Keyword */\\n.codehilite .o { color: #666666 } /* Operator */\\n.codehilite .ch { color: #408080; font-style: italic } /* Comment.Hashbang */\\n.codehilite .cm { color: #408080; font-style: italic } /* Comment.Multiline */\\n.codehilite .cp { color: #BC7A00 } /* Comment.Preproc */\\n.codehilite .cpf { color: #408080; font-style: italic } /* Comment.PreprocFile */\\n.codehilite .c1 { color: #408080; font-style: italic } /* Comment.Single */\\n.codehilite .cs { color: #408080; font-style: italic } /* Comment.Special */\\n.codehilite .gd { color: #A00000 } /* Generic.Deleted */\\n.codehilite .ge { font-style: italic } /* Generic.Emph */\\n.codehilite .gr { color: #FF0000 } /* Generic.Error */\\n.codehilite .gh { color: #000080; font-weight: bold } /* Generic.Heading */\\n.codehilite .gi { color: #00A000 } /* Generic.Inserted */\\n.codehilite .go { color: #888888 } /* Generic.Output */\\n.codehilite .gp { color: #000080; font-weight: bold } /* Generic.Prompt */\\n.codehilite .gs { font-weight: bold } /* Generic.Strong */\\n.codehilite .gu { color: #800080; font-weight: bold } /* Generic.Subheading */\\n.codehilite .gt { color: #0044DD } /* Generic.Traceback */\\n.codehilite .kc { color: #008000; font-weight: bold } /* Keyword.Constant */\\n.codehilite .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */\\n.codehilite .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */\\n.codehilite .kp { color: #008000 } /* Keyword.Pseudo */\\n.codehilite .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */\\n.codehilite .kt { color: #B00040 } /* Keyword.Type */\\n.codehilite .m { color: #666666 } /* Literal.Number */\\n.codehilite .s { color: #BA2121 } /* Literal.String */\\n.codehilite .na { color: #7D9029 } /* Name.Attribute */\\n.codehilite .nb { color: #008000 } /* Name.Builtin */\\n.codehilite .nc { color: #0000FF; font-weight: bold } /* Name.Class */\\n.codehilite .no { color: #880000 } /* Name.Constant */\\n.codehilite .nd { color: #AA22FF } /* Name.Decorator */\\n.codehilite .ni { color: #999999; font-weight: bold } /* Name.Entity */\\n.codehilite .ne { color: #D2413A; font-weight: bold } /* Name.Exception */\\n.codehilite .nf { color: #0000FF } /* Name.Function */\\n.codehilite .nl { color: #A0A000 } /* Name.Label */\\n.codehilite .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */\\n.codehilite .nt { color: #008000; font-weight: bold } /* Name.Tag */\\n.codehilite .nv { color: #19177C } /* Name.Variable */\\n.codehilite .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */\\n.codehilite .w { color: #bbbbbb } /* Text.Whitespace */\\n.codehilite .mb { color: #666666 } /* Literal.Number.Bin */\\n.codehilite .mf { color: #666666 } /* Literal.Number.Float */\\n.codehilite .mh { color: #666666 } /* Literal.Number.Hex */\\n.codehilite .mi { color: #666666 } /* Literal.Number.Integer */\\n.codehilite .mo { color: #666666 } /* Literal.Number.Oct */\\n.codehilite .sa { color: #BA2121 } /* Literal.String.Affix */\\n.codehilite .sb { color: #BA2121 } /* Literal.String.Backtick */\\n.codehilite .sc { color: #BA2121 } /* Literal.String.Char */\\n.codehilite .dl { color: #BA2121 } /* Literal.String.Delimiter */\\n.codehilite .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */\\n.codehilite .s2 { color: #BA2121 } /* Literal.String.Double */\\n.codehilite .se { color: #BB6622; font-weight: bold } /* Literal.String.Escape */\\n.codehilite .sh { color: #BA2121 } /* Literal.String.Heredoc */\\n.codehilite .si { color: #BB6688; font-weight: bold } /* Literal.String.Interpol */\\n.codehilite .sx { color: #008000 } /* Literal.String.Other */\\n.codehilite .sr { color: #BB6688 } /* Literal.String.Regex */\\n.codehilite .s1 { color: #BA2121 } /* Literal.String.Single */\\n.codehilite .ss { color: #19177C } /* Literal.String.Symbol */\\n.codehilite .bp { color: #008000 } /* Name.Builtin.Pseudo */\\n.codehilite .fm { color: #0000FF } /* Name.Function.Magic */\\n.codehilite .vc { color: #19177C } /* Name.Variable.Class */\\n.codehilite .vg { color: #19177C } /* Name.Variable.Global */\\n.codehilite .vi { color: #19177C } /* Name.Variable.Instance */\\n.codehilite .vm { color: #19177C } /* Name.Variable.Magic */\\n.codehilite .il { color: #666666 } /* Literal.Number.Integer.Long */\\n\\n.markdown h1 { margin-block-start: 0.34em }\\n.markdown h2 { margin-block-start: 0.42em }\\n.markdown h3 { margin-block-start: 0.5em }\\n.markdown h4 { margin-block-start: 0.67em }\\n.markdown h5 { margin-block-start: 0.84em }\\n.markdown h6 { margin-block-start: 1.17em }\\n.markdown ul { padding-inline-start: 2em }\\n.markdown ol { padding-inline-start: 2em }\\n.markdown strong { font-weight: 600 }\\n.markdown a { color: -webkit-link }\\n.markdown a { color: -moz-hyperlinkText }\\n\");\n", + " },\n", + " function(Bokeh) {\n", + " inject_raw_css(\"table.panel-df {\\n margin-left: auto;\\n margin-right: auto;\\n border: none;\\n border-collapse: collapse;\\n border-spacing: 0;\\n color: black;\\n font-size: 12px;\\n table-layout: fixed;\\n width: 100%;\\n}\\n\\n.panel-df tr, th, td {\\n text-align: right;\\n vertical-align: middle;\\n padding: 0.5em 0.5em !important;\\n line-height: normal;\\n white-space: normal;\\n max-width: none;\\n border: none;\\n}\\n\\n.panel-df tbody {\\n display: table-row-group;\\n vertical-align: middle;\\n border-color: inherit;\\n}\\n\\n.panel-df tbody tr:nth-child(odd) {\\n background: #f5f5f5;\\n}\\n\\n.panel-df thead {\\n border-bottom: 1px solid black;\\n vertical-align: bottom;\\n}\\n\\n.panel-df tr:hover {\\n background: lightblue !important;\\n cursor: pointer;\\n}\\n\");\n", + " },\n", + " function(Bokeh) {\n", + " Bokeh.set_log_level(\"info\");\n", + " },\n", + " \n", + " function(Bokeh) {\n", + " /* BEGIN panel.min.js */\n", + " /*!\n", + " * Copyright (c) 2012 - 2019, Anaconda, Inc., and Bokeh Contributors\n", + " * All rights reserved.\n", + " * \n", + " * Redistribution and use in source and binary forms, with or without modification,\n", + " * are permitted provided that the following conditions are met:\n", + " * \n", + " * Redistributions of source code must retain the above copyright notice,\n", + " * this list of conditions and the following disclaimer.\n", + " * \n", + " * Redistributions in binary form must reproduce the above copyright notice,\n", + " * this list of conditions and the following disclaimer in the documentation\n", + " * and/or other materials provided with the distribution.\n", + " * \n", + " * Neither the name of Anaconda nor the names of any contributors\n", + " * may be used to endorse or promote products derived from this software\n", + " * without specific prior written permission.\n", + " * \n", + " * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\n", + " * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\n", + " * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE\n", + " * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE\n", + " * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR\n", + " * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF\n", + " * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS\n", + " * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN\n", + " * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)\n", + " * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF\n", + " * THE POSSIBILITY OF SUCH DAMAGE.\n", + " */\n", + " (function(root, factory) {\n", + " factory(root[\"Bokeh\"]);\n", + " })(this, function(Bokeh) {\n", + " var define;\n", + " return (function(modules, entry, aliases, externals) {\n", + " if (Bokeh != null) {\n", + " return Bokeh.register_plugin(modules, entry, aliases, externals);\n", + " } else {\n", + " throw new Error(\"Cannot find Bokeh. You have to load it prior to loading plugins.\");\n", + " }\n", + " })\n", + " ({\n", + " \"aa4f566620\": function _(r,e,t){var n=(this&&this.__importStar||function(r){if(r&&r.__esModule)return r;var e={};if(null!=r)for(var t in r)Object.hasOwnProperty.call(r,t)&&(e[t]=r[t]);return e.default=r,e})(r(\"4d02676c49\"));t.Panel=n,r(\"@bokehjs/base\").register_models(n)},\n", + " \"4d02676c49\": function _(a,e,r){var o=a(\"ff4b91e885\");r.AcePlot=o.AcePlot;var t=a(\"12e90a1b7e\");r.Audio=t.Audio;var c=a(\"cf3b018c7a\");r.DeckGLPlot=c.DeckGLPlot;var d=a(\"70a2bb70ef\");r.HTML=d.HTML;var v=a(\"dac8d750fa\");r.JSON=v.JSON;var P=a(\"c81021c8fd\");r.KaTeX=P.KaTeX;var b=a(\"a93ded647d\");r.MathJax=b.MathJax;var l=a(\"98100899bc\");r.Player=l.Player;var f=a(\"d46f026c83\");r.PlotlyPlot=f.PlotlyPlot;var i=a(\"d9b3a262de\");r.Progress=i.Progress;var n=a(\"4b4afba86a\");r.State=n.State;var S=a(\"14b669e6fc\");r.VegaPlot=S.VegaPlot;var V=a(\"71a2bbec38\");r.Video=V.Video;var s=a(\"76bc93d621\");r.VideoStream=s.VideoStream,function(a){for(var e in a)r.hasOwnProperty(e)||(r[e]=a[e])}(a(\"63070bc9ce\"))},\n", + " \"ff4b91e885\": function _(t,e,o){var i,n=this&&this.__extends||(i=function(t,e){return(i=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var o in e)e.hasOwnProperty(o)&&(t[o]=e[o])})(t,e)},function(t,e){function o(){this.constructor=t}i(t,e),t.prototype=null===e?Object.create(e):(o.prototype=e.prototype,new o)}),r=(this&&this.__importStar||function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var o in t)Object.hasOwnProperty.call(t,o)&&(e[o]=t[o]);return e.default=t,e})(t(\"@bokehjs/core/properties\")),s=t(\"@bokehjs/models/layouts/html_box\"),a=t(\"@bokehjs/core/dom\");var c=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return n(e,t),e.prototype.initialize=function(){t.prototype.initialize.call(this),this._ace=window.ace,this._container=a.div({id:\"_\"+Math.random().toString(36).substr(2,9),style:{width:\"100%\",height:\"100%\"}})},e.prototype.connect_signals=function(){var e=this;t.prototype.connect_signals.call(this),this.connect(this.model.properties.code.change,function(){return e._update_code_from_model()}),this.connect(this.model.properties.theme.change,function(){return e._update_theme()}),this.connect(this.model.properties.language.change,function(){return e._update_language()}),this.connect(this.model.properties.annotations.change,function(){return e._add_annotations()}),this.connect(this.model.properties.readonly.change,function(){e._editor.setReadOnly(e.model.readonly)})},e.prototype.render=function(){var e=this;t.prototype.render.call(this),this._container!==this.el.childNodes[0]&&this.el.appendChild(this._container),this._container.textContent=this.model.code,this._editor=this._ace.edit(this._container.id),this._editor.setTheme(\"ace/theme/\"+this.model.theme),this._editor.session.setMode(\"ace/mode/\"+this.model.language),this._editor.setReadOnly(this.model.readonly),this._langTools=this._ace.require(\"ace/ext/language_tools\"),this._editor.setOptions({enableBasicAutocompletion:!0,enableSnippets:!0,fontFamily:\"monospace\"}),this._editor.on(\"change\",function(){return e._update_code_from_editor()})},e.prototype._update_code_from_model=function(){this._editor&&this._editor.getValue()!=this.model.code&&this._editor.setValue(this.model.code)},e.prototype._update_code_from_editor=function(){this._editor.getValue()!=this.model.code&&(this.model.code=this._editor.getValue())},e.prototype._update_theme=function(){this._editor.setTheme(\"ace/theme/\"+this.model.theme)},e.prototype._update_language=function(){this._editor.session.setMode(\"ace/mode/\"+this.model.language)},e.prototype._add_annotations=function(){this._editor.session.setAnnotations(this.model.annotations)},e.prototype.after_layout=function(){t.prototype.after_layout.call(this),this._editor.resize()},e.__name__=\"AcePlotView\",e}(t(\"ec60963462\").PanelHTMLBoxView);o.AcePlotView=c;var h=function(t){function e(e){return t.call(this,e)||this}return 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this._cache_count[i]=this._cache_count[i]+1,this._cache[i];var n=new h.Sizeable(e).bounded_to(this.sizing.size),s=r.sized(this.el,n,function(){var e=new h.Sizeable(r.content_size(t.el)),i=r.extents(t.el),o=i.border,n=i.padding;return e.grow_by(o).grow_by(n).map(Math.ceil)});return this._cache[i]=s,this._cache_count[i]=0,s},t.__name__=\"CachedVariadicBox\",t}(s.Layoutable);i.CachedVariadicBox=l;var d=function(e){function t(){return null!==e&&e.apply(this,arguments)||this}return n(t,e),t.prototype._update_layout=function(){var e=void 0!==this._prev_sizing_mode&&this._prev_sizing_mode!==this.model.sizing_mode;this._prev_sizing_mode=this.model.sizing_mode,this.layout=new l(this.el,this.model.sizing_mode,e),this.layout.set_sizing(this.box_sizing())},t.prototype.render=function(){e.prototype.render.call(this),c(this.markup_el,this.model)},t.__name__=\"PanelMarkupView\",t}(a.MarkupView);i.PanelMarkupView=d;var u=function(e){function t(){return null!==e&&e.apply(this,arguments)||this}return 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e=this;t.prototype.render.call(this),this.audioEl=document.createElement(\"audio\"),this.audioEl.controls=!0,this.audioEl.src=this.model.value,this.audioEl.currentTime=this.model.time,this.audioEl.loop=this.model.loop,null!=this.model.volume?this.audioEl.volume=this.model.volume/100:this.model.volume=100*this.audioEl.volume,this.audioEl.onpause=function(){return e.model.paused=!0},this.audioEl.onplay=function(){return e.model.paused=!1},this.audioEl.ontimeupdate=function(){return e.update_time(e)},this.audioEl.onvolumechange=function(){return e.update_volume(e)},this.el.appendChild(this.audioEl),this.model.paused||this.audioEl.play()},e.prototype.update_time=function(t){t._setting?t._setting=!1:Date.now()-t._time1&&\"number\"==typeof h[0]?l[u]=r.data[u].slice(c*h[1],c*h[1]+h[1]):l[u]=r.data[u][c]}a.push(l)}i.data=a}t&&this.updateDeck()},e.prototype._on_click_event=function(t){var e={coordinate:t.coordinate,lngLat:t.lngLat,index:t.index};this.model.clickState=e},e.prototype._on_hover_event=function(t){var e={coordinate:t.coordinate,lngLat:t.lngLat,index:t.index};this.model.hoverState=e},e.prototype._on_viewState_event=function(t){this.model.viewState=t.viewState},e.prototype.getData=function(){var t=this;return r(r({},this.model.data),{layers:this.model.layers,initialViewState:this.model.initialViewState,onViewStateChange:function(e){return t._on_viewState_event(e)},onClick:function(e){return t._on_click_event(e)},onHover:function(e){return t._on_hover_event(e)}})},e.prototype.updateDeck=function(){if(this.deckGL){var t=this.getData();if(d.updateDeck)d.updateDeck(t,this.deckGL);else{var e=this.jsonConverter.convert(t);this.deckGL.setProps(e)}}else this.render()},e.prototype.createDeck=function(t){var e,o=t.mapboxApiKey,n=t.container,i=t.jsonInput,a=t.tooltip;try{var s=this.jsonConverter.convert(i),c=u.makeTooltip(a);e=new d.DeckGL(r(r({},s),{map:f,mapboxApiAccessToken:o,container:n,getTooltip:c}))}catch(t){console.error(t)}return e},e.prototype.render=function(){t.prototype.render.call(this);var e=c.div({class:\"deckgl\"});_.set_size(e,this.model);var o=this.model.mapbox_api_key,n=this.model.tooltip,i=this.getData();d.createDeck?this.deckGL=d.createDeck({mapboxApiKey:o,container:e,jsonInput:i,tooltip:n}):this.deckGL=this.createDeck({mapboxApiKey:o,container:e,jsonInput:i,tooltip:n}),this.el.appendChild(e)},e.__name__=\"DeckGLPlotView\",e}(_.PanelHTMLBoxView);o.DeckGLPlotView=m;var k=function(t){function e(e){return t.call(this,e)||this}return i(e,t),e.init_DeckGLPlot=function(){this.prototype.default_view=m,this.define({data:[l.Any],data_sources:[l.Array,[]],clickState:[l.Any],hoverState:[l.Any],initialViewState:[l.Any],layers:[l.Array,[]],mapbox_api_key:[l.String],tooltip:[l.Any],viewState:[l.Any]}),this.override({height:400,width:600})},e.__name__=\"DeckGLPlot\",e.__module__=\"panel.models.deckgl\",e}(p.HTMLBox);o.DeckGLPlot=k,k.init_DeckGLPlot()},\n", + " \"27d3545a25\": function _(e,t,n){var i,r,l={fontFamily:'\"Helvetica Neue\", Helvetica, Arial, sans-serif',display:\"flex\",flex:\"wrap\",maxWidth:\"500px\",flexDirection:\"column\",zIndex:2};function a(){return document.createElement(\"div\")}function o(e){if(!e.picked)return null;if(e.object===i)return r;var t={html:c(e.object),style:l};return r=t,i=e.object,t}n.getTooltipDefault=o;var s=new Set([\"position\",\"index\"]);function c(e){var t=a();for(var n in e)if(!s.has(n)){var i=a();i.className=\"header\",i.textContent=n;var r=a();r.className=\"value\",r.textContent=u(e[n]);var l=a();f(l,i,r),l.appendChild(i),l.appendChild(r),t.appendChild(l)}return t.innerHTML}function f(e,t,n){Object.assign(t.style,{fontWeight:700,marginRight:\"10px\",flex:\"1 1 0%\"}),Object.assign(n.style,{flex:\"none\",maxWidth:\"250px\",overflow:\"hidden\",whiteSpace:\"nowrap\",textOverflow:\"ellipsis\"}),Object.assign(e.style,{display:\"flex\",flexDirection:\"row\",justifyContent:\"space-between\",alignItems:\"stretch\"})}function u(e){var t;if(Array.isArray(e)&&e.length>4)t=\"Array<\"+e.length+\">\";else if(\"string\"==typeof e)t=e;else if(\"number\"==typeof e)t=String(e);else try{t=JSON.stringify(e)}catch(e){t=\"\"}return t.length>50&&(t=t.slice(0,50)),t}function p(e,t){var n=e;for(var i in t)n=n.replace(\"{\"+i+\"}\",t[i]);return n}n.tabularize=c,n.toText=u,n.substituteIn=p,n.makeTooltip=function(e){return e?e.html||e.text?function(t){if(!t.picked)return null;var n={style:e.style||l};return e.html?n.html=p(e.html,t.object):n.text=p(e.text,t.object),n}:o:null}},\n", + " \"093eb75864\": function 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user-select:none;\",\"once\"==this.model.loop_policy?m.checked=!0:\"loop\"==this.model.loop_policy?f.checked=!0:y.checked=!0,this.loop_state.appendChild(m),this.loop_state.appendChild(_),this.loop_state.appendChild(f),this.loop_state.appendChild(v),this.loop_state.appendChild(y),this.loop_state.appendChild(x),this.el.appendChild(this.sliderEl),this.el.appendChild(i),this.el.appendChild(this.loop_state)},e.prototype.set_frame=function(t){this.model.value!=t&&(this.model.value=t),this.sliderEl.value!=String(t)&&(this.sliderEl.value=String(t))},e.prototype.get_loop_state=function(){for(var t=this.loop_state.state,e=0;e0?this.play_animation():this.model.direction<0&&this.reverse_animation()},e.prototype.faster=function(){this.model.interval=Math.round(.7*this.model.interval),this.model.direction>0?this.play_animation():this.model.direction<0&&this.reverse_animation()},e.prototype.anim_step_forward=function(){if(this.model.valuethis.model.start)this.previous_frame();else{var t=this.get_loop_state();\"loop\"==t?this.last_frame():\"reflect\"==t?(this.first_frame(),this.play_animation()):(this.pause_animation(),this.first_frame())}},e.prototype.pause_animation=function(){this.model.direction=0,this.timer&&(clearInterval(this.timer),this.timer=null)},e.prototype.play_animation=function(){var t=this;this.pause_animation(),this.model.direction=1,this.timer||(this.timer=setInterval(function(){return t.anim_step_forward()},this.model.interval))},e.prototype.reverse_animation=function(){var t=this;this.pause_animation(),this.model.direction=-1,this.timer||(this.timer=setInterval(function(){return t.anim_step_reverse()},this.model.interval))},e.__name__=\"PlayerView\",e}(a.WidgetView);i.PlayerView=l;var d=function(t){function e(e){return t.call(this,e)||this}return o(e,t),e.init_Player=function(){this.prototype.default_view=l,this.define({direction:[r.Number,0],interval:[r.Number,500],start:[r.Number],end:[r.Number],step:[r.Number,1],loop_policy:[r.Any,\"once\"],value:[r.Any,0]}),this.override({width:400})},e.__name__=\"Player\",e.__module__=\"panel.models.widgets\",e}(a.Widget);i.Player=d,d.init_Player()},\n", + " \"d46f026c83\": function _(t,e,o){var r,n=this&&this.__extends||(r=function(t,e){return(r=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var o in e)e.hasOwnProperty(o)&&(t[o]=e[o])})(t,e)},function(t,e){function o(){this.constructor=t}r(t,e),t.prototype=null===e?Object.create(e):(o.prototype=e.prototype,new o)}),i=(this&&this.__importStar||function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var o in t)Object.hasOwnProperty.call(t,o)&&(e[o]=t[o]);return e.default=t,e})(t(\"@bokehjs/core/properties\")),l=t(\"@bokehjs/core/util/object\"),a=t(\"@bokehjs/core/util/eq\"),p=t(\"@bokehjs/models/layouts/html_box\"),s=t(\"99a25e6992\"),u=t(\"62ba79515f\"),c=t(\"ec60963462\"),_=window.Plotly,d=function(t,e,o){var r=Array.isArray(e)?[]:{};if(\"click\"===o||\"hover\"===o||\"selected\"===o){var n=[];if(null==e)return null;for(var i=t.data,l=0;l1){for(var u=[],c=0;c=0?t=setTimeout(i,l-c):(t=null,u||(r=n.apply(o,e),o=e=null))}null==l&&(l=100);var c=function(){o=this,e=arguments,a=Date.now();var c=u&&!t;return t||(t=setTimeout(i,l)),c&&(r=n.apply(o,e),o=e=null),r};return c.clear=function(){t&&(clearTimeout(t),t=null)},c.flush=function(){t&&(r=n.apply(o,e),o=e=null,clearTimeout(t),t=null)},c}t.debounce=t,l.exports=t},\n", + " \"62ba79515f\": function _(t,r,n){n.get=function(t,r,n){void 0===n&&(n=void 0);var e=function(n){return String.prototype.split.call(r,n).filter(Boolean).reduce(function(t,r){return null!=t?t[r]:t},t)},o=e(/[,[\\]]+?/)||e(/[,[\\].]+?/);return void 0===o||o===t?n:o},n.throttle=function(t,r){var n=0;return function(){var e=Number(new Date);e-n>=r&&(t(),n=e)}},n.deepCopy=function t(r){var n;if(null==r||\"object\"!=typeof r)return r;if(r instanceof Array){n=[];for(var e=0,o=r.length;e0){var t=this._fetch_datasets();if(\"data\"in t&&(this.model.data.data.values=t.data,delete t.data),void 0!==this.model.data.data)for(var e=0,o=this.model.data.data;e0&&(this.timer=setInterval(function(){return t.snapshot()},this.model.timeout))},e.prototype.snapshot=function(){this.canvasEl.width=this.videoEl.videoWidth,this.canvasEl.height=this.videoEl.videoHeight;var t=this.canvasEl.getContext(\"2d\");t&&t.drawImage(this.videoEl,0,0,this.canvasEl.width,this.canvasEl.height),this.model.value=this.canvasEl.toDataURL(\"image/\"+this.model.format,.95)},e.prototype.remove=function(){t.prototype.remove.call(this),this.timer&&(clearInterval(this.timer),this.timer=null)},e.prototype.render=function(){var e=this;t.prototype.render.call(this),this.videoEl||(this.videoEl=document.createElement(\"video\"),this.model.sizing_mode&&\"fixed\"!==this.model.sizing_mode||(this.model.height&&(this.videoEl.height=this.model.height),this.model.width&&(this.videoEl.width=this.model.width)),this.videoEl.style.objectFit=\"fill\",this.videoEl.style.minWidth=\"100%\",this.videoEl.style.minHeight=\"100%\",this.canvasEl=document.createElement(\"canvas\"),this.el.appendChild(this.videoEl),navigator.mediaDevices.getUserMedia&&navigator.mediaDevices.getUserMedia(this.constraints).then(function(t){e.videoEl.srcObject=t,e.model.paused||e.videoEl.play()}).catch(console.error))},e.__name__=\"VideoStreamView\",e}(t(\"ec60963462\").PanelHTMLBoxView);i.VideoStreamView=h;var a=function(t){function e(e){return t.call(this,e)||this}return n(e,t),e.init_VideoStream=function(){this.prototype.default_view=h,this.define({format:[s.String,\"png\"],paused:[s.Boolean,!1],snapshot:[s.Boolean,!1],timeout:[s.Number,0],value:[s.Any]}),this.override({height:240,width:320})},e.__name__=\"VideoStream\",e.__module__=\"panel.models.widgets\",e}(r.HTMLBox);i.VideoStream=a,a.init_VideoStream()},\n", + " \"63070bc9ce\": function _(V,o,e){var l=V(\"1a4b530306\");e.VTKPlot=l.VTKPlot;var K=V(\"b933e81f56\");e.VTKVolumePlot=K.VTKVolumePlot;var T=V(\"5bc27423fe\");e.VTKAxes=T.VTKAxes},\n", + " \"1a4b530306\": function _(e,t,n){var i,o=this&&this.__extends||(i=function(e,t){return(i=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(e,t){e.__proto__=t}||function(e,t){for(var n in t)t.hasOwnProperty(n)&&(e[n]=t[n])})(e,t)},function(e,t){function n(){this.constructor=e}i(e,t),e.prototype=null===t?Object.create(t):(n.prototype=t.prototype,new n)}),r=(this&&this.__importStar||function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t})(e(\"@bokehjs/core/properties\")),a=e(\"@bokehjs/core/dom\"),s=e(\"7620c2cc05\"),c=e(\"3b847a648d\"),d=function(e){function t(){var t=null!==e&&e.apply(this,arguments)||this;return t._axes_initialized=!1,t}return o(t,e),t.prototype.connect_signals=function(){var t=this;e.prototype.connect_signals.call(this),this.connect(this.model.properties.axes.change,function(){t._delete_axes(),t.model.axes&&t._set_axes(),t._vtk_renwin.getRenderWindow().render()}),this.el.addEventListener(\"mouseenter\",function(){var e=t._vtk_renwin.getInteractor();t.model.enable_keybindings&&(document.querySelector(\"body\").addEventListener(\"keypress\",e.handleKeyPress),document.querySelector(\"body\").addEventListener(\"keydown\",e.handleKeyDown),document.querySelector(\"body\").addEventListener(\"keyup\",e.handleKeyUp))}),this.el.addEventListener(\"mouseleave\",function(){var e=t._vtk_renwin.getInteractor();document.querySelector(\"body\").removeEventListener(\"keypress\",e.handleKeyPress),document.querySelector(\"body\").removeEventListener(\"keydown\",e.handleKeyDown),document.querySelector(\"body\").removeEventListener(\"keyup\",e.handleKeyUp)})},t.prototype.render=function(){e.prototype.render.call(this),this._axes=null,this._axes_initialized=!1,this._plot()},t.prototype.after_layout=function(){this._axes_initialized||(this._render_axes_canvas(),this._axes_initialized=!0)},t.prototype._render_axes_canvas=function(){var e=this,t=this._vtk_container.getElementsByTagName(\"canvas\");if(1!=t.length)throw Error(\"Error at initialization of the 3D scene, container should have one and only one canvas\");t[0].classList.add(\"scene3d-canvas\");var n=a.canvas({style:{position:\"absolute\",top:\"0\",left:\"0\",width:\"100%\",height:\"100%\"}});n.classList.add(\"axes-canvas\"),this._vtk_container.appendChild(n),this._vtk_renwin.setResizeCallback(function(){var t=e._vtk_container.getBoundingClientRect(),i=Math.floor(t.width*window.devicePixelRatio),o=Math.floor(t.height*window.devicePixelRatio);n.setAttribute(\"width\",i.toFixed()),n.setAttribute(\"height\",o.toFixed())})},t.prototype._delete_axes=function(){var e=this;if(null!=this._axes){Object.keys(this._axes).forEach(function(t){return e._vtk_renwin.getRenderer().removeActor(e._axes[t])});var t=this._vtk_renwin.getContainer().getElementsByClassName(\"axes-canvas\")[0],n=t.getContext(\"2d\");n&&n.clearRect(0,0,t.clientWidth*window.devicePixelRatio,t.clientHeight*window.devicePixelRatio),this._axes=null}},t.prototype._set_axes=function(){if(this.model.axes){var e=this._vtk_renwin.getContainer().getElementsByClassName(\"axes-canvas\")[0],t=this.model.axes.create_axes(e),n=t.psActor,i=t.axesActor,o=t.gridActor;this._axes={psActor:n,axesActor:i,gridActor:o},this._vtk_renwin.getRenderer().addActor(n),this._vtk_renwin.getRenderer().addActor(i),this._vtk_renwin.getRenderer().addActor(o)}},t.prototype._plot=function(){var e=this;if(this.model.data)var t=c.vtkns.DataAccessHelper.get(\"zip\",{zipContent:atob(this.model.data),callback:function(n){var i=c.vtkns.HttpSceneLoader.newInstance({renderer:e._vtk_renwin.getRenderer(),dataAccessHelper:t}),o=c.vtk.macro.debounce(function(){null==e._axes&&e.model.axes&&e._set_axes(),e.model.properties.camera.change.emit()},100);i.setUrl(\"index.json\"),i.onReady(o)}});else this._vtk_renwin.getRenderWindow().render()},t.__name__=\"VTKPlotView\",t}(s.AbstractVTKView);n.VTKPlotView=d;var l=function(e){function t(t){var n=e.call(this,t)||this;n.outline=c.vtkns.OutlineFilter.newInstance();var i=c.vtkns.Mapper.newInstance();return i.setInputConnection(n.outline.getOutputPort()),n.outline_actor=c.vtkns.Actor.newInstance(),n.outline_actor.setMapper(i),n}return o(t,e),t.init_VTKPlot=function(){this.prototype.default_view=d,this.define({data:[r.String],axes:[r.Instance],enable_keybindings:[r.Boolean,!1]})},t.__name__=\"VTKPlot\",t}(s.AbstractVTKPlot);n.VTKPlot=l,l.init_VTKPlot()},\n", + " \"7620c2cc05\": function _(e,t,n){var i,r=this&&this.__extends||(i=function(e,t){return(i=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(e,t){e.__proto__=t}||function(e,t){for(var n in t)t.hasOwnProperty(n)&&(e[n]=t[n])})(e,t)},function(e,t){function n(){this.constructor=e}i(e,t),e.prototype=null===t?Object.create(t):(n.prototype=t.prototype,new n)}),o=(this&&this.__importStar||function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t})(e(\"@bokehjs/core/properties\")),a=e(\"@bokehjs/core/dom\"),s=e(\"@bokehjs/core/util/object\"),_=e(\"@bokehjs/models/layouts/html_box\"),c=e(\"ec60963462\"),d=e(\"3b847a648d\"),h=function(e){function t(){var t=null!==e&&e.apply(this,arguments)||this;return t._setting_camera=!1,t}return r(t,e),t.prototype.connect_signals=function(){var t=this;e.prototype.connect_signals.call(this),this.connect(this.model.properties.data.change,function(){t.invalidate_render()}),this.connect(this.model.properties.orientation_widget.change,function(){t._orientation_widget_visibility(t.model.orientation_widget)}),this.connect(this.model.properties.camera.change,function(){return t._set_camera_state()})},t.prototype._orientation_widget_visibility=function(e){this._orientationWidget.setEnabled(e),e?this._widgetManager.enablePicking():this._widgetManager.disablePicking(),this._orientationWidget.updateMarkerOrientation(),this._vtk_renwin.getRenderWindow().render()},t.prototype._create_orientation_widget=function(){var e=this,t=d.vtkns.AxesActor.newInstance(),n=d.vtkns.OrientationMarkerWidget.newInstance({actor:t,interactor:this._vtk_renwin.getInteractor()});n.setEnabled(!0),n.setViewportCorner(d.vtkns.OrientationMarkerWidget.Corners.BOTTOM_RIGHT),n.setViewportSize(.15),n.setMinPixelSize(100),n.setMaxPixelSize(300),this._orientationWidget=n;var i=d.vtkns.WidgetManager.newInstance();i.setRenderer(n.getRenderer());var r=d.vtkns.InteractiveOrientationWidget.newInstance();r.placeWidget(t.getBounds()),r.setBounds(t.getBounds()),r.setPlaceFactor(1);var o=i.addWidget(r);this._widgetManager=i,o.onOrientationChange(function(t){var n=t.direction,i=e._vtk_renwin.getRenderer().getActiveCamera(),r=i.getFocalPoint(),o=i.getPosition(),a=i.getViewUp(),s=Math.sqrt(Math.pow(o[0]-r[0],2)+Math.pow(o[1]-r[1],2)+Math.pow(o[2]-r[2],2));i.setPosition(r[0]+n[0]*s,r[1]+n[1]*s,r[2]+n[2]*s),n[0]&&i.setViewUp(d.majorAxis(a,1,2)),n[1]&&i.setViewUp(d.majorAxis(a,0,2)),n[2]&&i.setViewUp(d.majorAxis(a,0,1)),e._orientationWidget.updateMarkerOrientation(),e._vtk_renwin.getRenderer().resetCameraClippingRange(),e._vtk_renwin.getRenderWindow().render()}),this._orientation_widget_visibility(this.model.orientation_widget)},t.prototype._get_camera_state=function(){if(!this._setting_camera){this._setting_camera=!0;var e=s.clone(this._vtk_renwin.getRenderer().getActiveCamera().get());delete e.classHierarchy,delete e.vtkObject,delete e.vtkCamera,delete e.viewPlaneNormal,this.model.camera=e,this._setting_camera=!1}},t.prototype._set_camera_state=function(){if(!this._setting_camera){this._setting_camera=!0;try{this.model.camera&&this._vtk_renwin.getRenderer().getActiveCamera().set(this.model.camera)}finally{this._setting_camera=!1}this._orientationWidget.updateMarkerOrientation(),this._vtk_renwin.getRenderer().resetCameraClippingRange(),this._vtk_renwin.getRenderWindow().render()}},t.prototype.render=function(){var t=this;e.prototype.render.call(this),this._orientationWidget=null,this._vtk_container=a.div(),c.set_size(this._vtk_container,this.model),this.el.appendChild(this._vtk_container),this._vtk_renwin=d.vtkns.FullScreenRenderWindow.newInstance({rootContainer:this.el,container:this._vtk_container}),this._remove_default_key_binding(),this._create_orientation_widget(),this._vtk_renwin.getRenderer().getActiveCamera().onModified(function(){return t._get_camera_state()}),this._set_camera_state(),this.model.renderer_el=this._vtk_renwin},t.prototype.after_layout=function(){e.prototype.after_layout.call(this),this._vtk_renwin.resize()},t.prototype._remove_default_key_binding=function(){var e=this._vtk_renwin.getInteractor();document.querySelector(\"body\").removeEventListener(\"keypress\",e.handleKeyPress),document.querySelector(\"body\").removeEventListener(\"keydown\",e.handleKeyDown),document.querySelector(\"body\").removeEventListener(\"keyup\",e.handleKeyUp)},t.__name__=\"AbstractVTKView\",t}(c.PanelHTMLBoxView);n.AbstractVTKView=h;var l=function(e){function t(t){return e.call(this,t)||this}return r(t,e),t.prototype.getActors=function(){return this.renderer_el.getRenderer().getActors()},t.init_AbstractVTKPlot=function(){this.define({orientation_widget:[o.Boolean,!1],camera:[o.Instance]}),this.override({height:300,width:300})},t.__name__=\"AbstractVTKPlot\",t.__module__=\"panel.models.vtk\",t}(_.HTMLBox);n.AbstractVTKPlot=l,l.init_AbstractVTKPlot()},\n", + " \"3b847a648d\": function _(e,t,n){var r=e(\"@bokehjs/core/util/serialization\"),a=e(\"@bokehjs/core/util/array\");function o(e){var t=Math.min(Math.max(Math.round(e),0),255).toString(16);return 2==t.length?t:\"0\"+t}function i(e,t,n){return\"#\"+o(e)+o(t)+o(n)}function v(e){for(var t=new ArrayBuffer(e.length),n=new Uint8Array(t),r=0,a=e.length;rMath.abs(e[n])?t:n,o=e[a]>0?1:-1;return r[a]=o,r},n.cartesian_product=function(){for(var e=[],t=0;t=.005&&(e.model.sampling=t)}),Math.abs(this.model.sampling-Number(this.shadow_selector.value))>=.005&&this.model.properties.sampling.change.emit(),this.edge_gradient_slider.addEventListener(\"input\",function(){var t=Number(e.edge_gradient_slider.value);Math.abs(e.model.edge_gradient-t)>=.005&&(e.model.edge_gradient=t)}),Math.abs(this.model.edge_gradient-Number(this.edge_gradient_slider.value))>=.005&&this.model.properties.edge_gradient.change.emit()},t.prototype._plot_volume=function(){var e=this,t=this._vtk_image_data,n=a.vtkns.Volume.newInstance(),r=a.vtkns.VolumeMapper.newInstance();n.setMapper(r),r.setInputData(t);var i=(t.getPointData().getScalars()||t.getPointData().getArrays()[0]).getRange(),o=a.vtkns.ColorTransferFunction.newInstance();o.onModified(function(){return e.model.mapper=a.vtkLutToMapper(o)});var s=a.vtkns.PiecewiseFunction.newInstance(),l=.7*Math.sqrt(t.getSpacing().map(function(e){return e*e}).reduce(function(e,t){return e+t},0));r.setSampleDistance(l),n.getProperty().setRGBTransferFunction(0,o),n.getProperty().setScalarOpacity(0,s),n.getProperty().setInterpolationTypeToFastLinear(),n.getProperty().setScalarOpacityUnitDistance(0,a.vtkns.BoundingBox.getDiagonalLength(t.getBounds())/Math.max.apply(Math,t.getDimensions())),n.getProperty().setGradientOpacityMinimumValue(0,0),n.getProperty().setGradientOpacityMaximumValue(0,.05*(i[1]-i[0])),n.getProperty().setShade(this.model.shadow),n.getProperty().setUseGradientOpacity(0,!0),n.getProperty().setGradientOpacityMinimumOpacity(0,0),n.getProperty().setGradientOpacityMaximumOpacity(0,1),n.getProperty().setAmbient(this.model.ambient),n.getProperty().setDiffuse(this.model.diffuse),n.getProperty().setSpecular(this.model.specular),n.getProperty().setSpecularPower(this.model.specular_power),this._vtk_renwin.getRenderer().addVolume(n),this._controllerWidget.setupContent(this._vtk_renwin.getRenderWindow(),n,!0)},t.prototype._plot_slices=function(){var e=this._vtk_image_data,t=a.vtkns.ImageSlice.newInstance(),n=a.vtkns.ImageSlice.newInstance(),r=a.vtkns.ImageSlice.newInstance(),i=a.vtkns.ImageMapper.newInstance(),o=a.vtkns.ImageMapper.newInstance(),s=a.vtkns.ImageMapper.newInstance();i.setInputData(e),i.setISlice(this.model.slice_i),t.setMapper(i),o.setInputData(e),o.setJSlice(this.model.slice_j),n.setMapper(o),s.setInputData(e),s.setKSlice(this.model.slice_k),r.setMapper(s);var l=a.vtkns.PiecewiseFunction.newInstance();l.removeAllPoints(),l.addPoint(0,1);var c=this.volume.getProperty().getRGBTransferFunction(0),p=t.getProperty();n.setProperty(p),r.setProperty(p),p.setRGBTransferFunction(c),p.setScalarOpacity(l);var d=this._vtk_renwin.getRenderer();d.addActor(t),d.addActor(n),d.addActor(r)},t.prototype._set_volume_visibility=function(e){this.volume.setVisibility(e)},t.prototype._set_slices_visibility=function(e){this._vtk_renwin.getRenderer().getActors().map(function(t){return t.setVisibility(e)})},t.__name__=\"VTKVolumePlotView\",t}(s.AbstractVTKView);n.VTKVolumePlotView=l;var c=function(e){function t(t){return e.call(this,t)||this}return i(t,e),t.init_VTKVolumePlot=function(){this.prototype.default_view=l,this.define({data:[o.Instance],shadow:[o.Boolean,!0],sampling:[o.Number,.4],edge_gradient:[o.Number,.2],colormap:[o.String],rescale:[o.Boolean,!1],ambient:[o.Number,.2],diffuse:[o.Number,.7],specular:[o.Number,.3],specular_power:[o.Number,8],slice_i:[o.Int,0],slice_j:[o.Int,0],slice_k:[o.Int,0],display_volume:[o.Boolean,!0],display_slices:[o.Boolean,!1],render_background:[o.String,\"#52576e\"],interpolation:[o.Any,\"fast_linear\"],mapper:[o.Instance]})},t.__name__=\"VTKVolumePlot\",t}(s.AbstractVTKPlot);n.VTKVolumePlot=c,c.init_VTKVolumePlot()},\n", + " \"5bc27423fe\": function _(t,e,i){var s,n=this&&this.__extends||(s=function(t,e){return(s=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var i in 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t[0]=(1-(l+m))*S,t[1]=(c+P)*S,t[2]=(b-y)*S,t[3]=0,t[4]=(c-P)*O,t[5]=(1-(f+m))*O,t[6]=(v+p)*O,t[7]=0,t[8]=(b+y)*E,t[9]=(v-p)*E,t[10]=(1-(f+l))*E,t[11]=0,t[12]=n[0],t[13]=n[1],t[14]=n[2],t[15]=1,t},n.fromRotationTranslationScaleOrigin=function(t,a,n,r,o){var e=a[0],u=a[1],h=a[2],i=a[3],M=e+e,s=u+u,f=h+h,c=e*M,b=e*s,l=e*f,v=u*s,m=u*f,p=h*f,y=i*M,P=i*s,S=i*f,O=r[0],E=r[1],I=r[2],L=o[0],N=o[1],R=o[2],x=(1-(v+p))*O,d=(b+S)*O,g=(l-P)*O,A=(b-S)*E,Y=(1-(c+p))*E,T=(m+y)*E,w=(l+P)*I,_=(m-y)*I,q=(1-(c+v))*I;return t[0]=x,t[1]=d,t[2]=g,t[3]=0,t[4]=A,t[5]=Y,t[6]=T,t[7]=0,t[8]=w,t[9]=_,t[10]=q,t[11]=0,t[12]=n[0]+L-(x*L+A*N+w*R),t[13]=n[1]+N-(d*L+Y*N+_*R),t[14]=n[2]+R-(g*L+T*N+q*R),t[15]=1,t},n.fromQuat=function(t,a){var n=a[0],r=a[1],o=a[2],e=a[3],u=n+n,h=r+r,i=o+o,M=n*u,s=r*u,f=r*h,c=o*u,b=o*h,l=o*i,v=e*u,m=e*h,p=e*i;return t[0]=1-f-l,t[1]=s+p,t[2]=c-m,t[3]=0,t[4]=s-p,t[5]=1-M-l,t[6]=b+v,t[7]=0,t[8]=c+m,t[9]=b-v,t[10]=1-M-f,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,t},n.frustum=function(t,a,n,r,o,e,u){var h=1/(n-a),i=1/(o-r),M=1/(e-u);return t[0]=2*e*h,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=2*e*i,t[6]=0,t[7]=0,t[8]=(n+a)*h,t[9]=(o+r)*i,t[10]=(u+e)*M,t[11]=-1,t[12]=0,t[13]=0,t[14]=u*e*2*M,t[15]=0,t},n.perspective=function(t,a,n,r,o){var e,u=1/Math.tan(a/2);t[0]=u/n,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=u,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[11]=-1,t[12]=0,t[13]=0,t[15]=0,null!=o&&o!==1/0?(e=1/(r-o),t[10]=(o+r)*e,t[14]=2*o*r*e):(t[10]=-1,t[14]=-2*r);return t},n.perspectiveFromFieldOfView=function(t,a,n,r){var o=Math.tan(a.upDegrees*Math.PI/180),e=Math.tan(a.downDegrees*Math.PI/180),u=Math.tan(a.leftDegrees*Math.PI/180),h=Math.tan(a.rightDegrees*Math.PI/180),i=2/(u+h),M=2/(o+e);return t[0]=i,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=M,t[6]=0,t[7]=0,t[8]=-(u-h)*i*.5,t[9]=(o-e)*M*.5,t[10]=r/(n-r),t[11]=-1,t[12]=0,t[13]=0,t[14]=r*n/(n-r),t[15]=0,t},n.ortho=function(t,a,n,r,o,e,u){var h=1/(a-n),i=1/(r-o),M=1/(e-u);return t[0]=-2*h,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=-2*i,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[10]=2*M,t[11]=0,t[12]=(a+n)*h,t[13]=(o+r)*i,t[14]=(u+e)*M,t[15]=1,t},n.lookAt=function(t,a,n,r){var e,h,i,M,s,f,c,b,l,v,m=a[0],p=a[1],y=a[2],P=r[0],S=r[1],O=r[2],E=n[0],I=n[1],L=n[2];if(Math.abs(m-E)0&&(b=1/Math.sqrt(b),s*=b,f*=b,c*=b);var l=i*c-M*f,v=M*s-h*c,m=h*f-i*s;(b=l*l+v*v+m*m)>0&&(b=1/Math.sqrt(b),l*=b,v*=b,m*=b);return t[0]=l,t[1]=v,t[2]=m,t[3]=0,t[4]=f*m-c*v,t[5]=c*l-s*m,t[6]=s*v-f*l,t[7]=0,t[8]=s,t[9]=f,t[10]=c,t[11]=0,t[12]=o,t[13]=e,t[14]=u,t[15]=1,t},n.str=function(t){return\"mat4(\"+t[0]+\", \"+t[1]+\", \"+t[2]+\", \"+t[3]+\", \"+t[4]+\", \"+t[5]+\", \"+t[6]+\", \"+t[7]+\", \"+t[8]+\", \"+t[9]+\", \"+t[10]+\", \"+t[11]+\", \"+t[12]+\", \"+t[13]+\", \"+t[14]+\", 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\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
    \\n\"+\n \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n \"
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    • \\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"\"}};\n\n function display_loaded() {\n var el = document.getElementById(\"1001\");\n if (el != null) {\n el.textContent = \"BokehJS is loading...\";\n }\n if (root.Bokeh !== undefined) {\n if (el != null) {\n el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(display_loaded, 100)\n }\n }\n\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };var element = document.getElementById(\"1001\");\n if (element == null) {\n console.error(\"Bokeh: ERROR: autoload.js configured with elementid '1001' but no matching script tag was found. \")\n return false;\n }\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n \n var js_urls = [\"https://cdn.pydata.org/bokeh/release/bokeh-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-tables-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-gl-1.4.0.min.js\"];\n var css_urls = [];\n \n\n var inline_js = [\n function(Bokeh) {\n inject_raw_css(\".widget-box {\\n\\tmin-height: 20px;\\n\\tbackground-color: #f5f5f5;\\n\\tborder: 1px solid #e3e3e3 !important;\\n\\tborder-radius: 4px;\\n\\t-webkit-box-shadow: inset 0 1px 1px rgba(0,0,0,.05);\\n\\tbox-shadow: inset 0 1px 1px rgba(0,0,0,.05);\\n\\toverflow-x: hidden;\\n\\toverflow-y: hidden;\\n}\\n\\n.scrollable {\\n overflow: scroll;\\n}\\n\\nprogress {\\n\\tappearance: none;\\n\\t-moz-appearance: none;\\n\\t-webkit-appearance: none;\\n\\n\\tborder: none;\\n\\theight: 20px;\\n\\tbackground-color: whiteSmoke;\\n\\tborder-radius: 3px;\\n\\tbox-shadow: 0 2px 3px rgba(0,0,0,.5) inset;\\n\\tcolor: royalblue;\\n\\tposition: relative;\\n\\tmargin: 0 0 1.5em;\\n}\\n\\nprogress[value]::-webkit-progress-bar {\\n\\tbackground-color: whiteSmoke;\\n\\tborder-radius: 3px;\\n\\tbox-shadow: 0 2px 3px rgba(0,0,0,.5) inset;\\n}\\n\\nprogress[value]::-webkit-progress-value {\\n\\tposition: relative;\\n\\n\\tbackground-size: 35px 20px, 100% 100%, 100% 100%;\\n\\tborder-radius:3px;\\n}\\n\\nprogress.active:not([value])::before {\\n\\tbackground-position: 10%;\\n\\tanimation-name: stripes;\\n\\tanimation-duration: 3s;\\n\\tanimation-timing-function: linear;\\n\\tanimation-iteration-count: infinite;\\n}\\n\\nprogress[value]::-moz-progress-bar {\\n\\tbackground-size: 35px 20px, 100% 100%, 100% 100%;\\n\\tborder-radius:3px;\\n}\\n\\nprogress:not([value])::-moz-progress-bar {\\n\\tborder-radius:3px;\\n\\tbackground:\\n\\tlinear-gradient(-45deg, transparent 33%, rgba(0, 0, 0, 0.2) 33%, rgba(0, 0, 0, 0.2) 66%, transparent 66%) left/2.5em 1.5em;\\n\\n}\\n\\nprogress.active:not([value])::-moz-progress-bar {\\n\\tbackground-position: 10%;\\n\\tanimation-name: stripes;\\n\\tanimation-duration: 3s;\\n\\tanimation-timing-function: linear;\\n\\tanimation-iteration-count: infinite;\\n}\\n\\nprogress.active:not([value])::-webkit-progress-bar {\\n\\tbackground-position: 10%;\\n\\tanimation-name: stripes;\\n\\tanimation-duration: 3s;\\n\\tanimation-timing-function: linear;\\n\\tanimation-iteration-count: infinite;\\n}\\n\\nprogress.primary[value]::-webkit-progress-value { background-color: #007bff; }\\nprogress.primary:not([value])::before { background-color: #007bff; }\\nprogress.primary:not([value])::-webkit-progress-bar { background-color: #007bff; }\\nprogress.primary::-moz-progress-bar { background-color: #007bff; }\\n\\nprogress.secondary[value]::-webkit-progress-value { background-color: #6c757d; }\\nprogress.secondary:not([value])::before { background-color: #6c757d; }\\nprogress.secondary:not([value])::-webkit-progress-bar { background-color: #6c757d; }\\nprogress.secondary::-moz-progress-bar { background-color: #6c757d; }\\n\\nprogress.success[value]::-webkit-progress-value { background-color: #28a745; }\\nprogress.success:not([value])::before { background-color: #28a745; }\\nprogress.success:not([value])::-webkit-progress-bar { background-color: #28a745; }\\nprogress.success::-moz-progress-bar { background-color: #28a745; }\\n\\nprogress.danger[value]::-webkit-progress-value { background-color: #dc3545; }\\nprogress.danger:not([value])::before { background-color: #dc3545; }\\nprogress.danger:not([value])::-webkit-progress-bar { background-color: #dc3545; }\\nprogress.danger::-moz-progress-bar { background-color: #dc3545; }\\n\\nprogress.warning[value]::-webkit-progress-value { background-color: #ffc107; }\\nprogress.warning:not([value])::before { background-color: #ffc107; }\\nprogress.warning:not([value])::-webkit-progress-bar { background-color: #ffc107; }\\nprogress.warning::-moz-progress-bar { background-color: #ffc107; }\\n\\nprogress.info[value]::-webkit-progress-value { background-color: #17a2b8; }\\nprogress.info:not([value])::before { background-color: #17a2b8; }\\nprogress.info:not([value])::-webkit-progress-bar { background-color: #17a2b8; }\\nprogress.info::-moz-progress-bar { background-color: #17a2b8; }\\n\\nprogress.light[value]::-webkit-progress-value { background-color: #f8f9fa; }\\nprogress.light:not([value])::before { background-color: #f8f9fa; }\\nprogress.light:not([value])::-webkit-progress-bar { background-color: #f8f9fa; }\\nprogress.light::-moz-progress-bar { background-color: #f8f9fa; }\\n\\nprogress.dark[value]::-webkit-progress-value { background-color: #343a40; }\\nprogress.dark:not([value])::-webkit-progress-bar { background-color: #343a40; }\\nprogress.dark:not([value])::before { background-color: #343a40; }\\nprogress.dark::-moz-progress-bar { background-color: #343a40; }\\n\\nprogress:not([value])::-webkit-progress-bar {\\n\\tborder-radius: 3px;\\n\\tbackground:\\n\\tlinear-gradient(-45deg, transparent 33%, rgba(0, 0, 0, 0.2) 33%, rgba(0, 0, 0, 0.2) 66%, transparent 66%) left/2.5em 1.5em;\\n}\\nprogress:not([value])::before {\\n\\tcontent:\\\" \\\";\\n\\tposition:absolute;\\n\\theight: 20px;\\n\\ttop:0;\\n\\tleft:0;\\n\\tright:0;\\n\\tbottom:0;\\n\\tborder-radius: 3px;\\n\\tbackground:\\n\\tlinear-gradient(-45deg, transparent 33%, rgba(0, 0, 0, 0.2) 33%, rgba(0, 0, 0, 0.2) 66%, transparent 66%) left/2.5em 1.5em;\\n}\\n\\n@keyframes stripes {\\n from {background-position: 0%}\\n to {background-position: 100%}\\n}\");\n },\n function(Bokeh) {\n inject_raw_css(\".json-formatter-row {\\n font-family: monospace;\\n}\\n.json-formatter-row,\\n.json-formatter-row a,\\n.json-formatter-row a:hover {\\n color: black;\\n text-decoration: none;\\n}\\n.json-formatter-row .json-formatter-row {\\n margin-left: 1rem;\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty {\\n opacity: 0.5;\\n margin-left: 1rem;\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty:after {\\n display: none;\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-object:after {\\n content: \\\"No properties\\\";\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-array:after {\\n content: \\\"[]\\\";\\n}\\n.json-formatter-row .json-formatter-string,\\n.json-formatter-row .json-formatter-stringifiable {\\n color: green;\\n white-space: pre;\\n word-wrap: break-word;\\n}\\n.json-formatter-row .json-formatter-number {\\n color: blue;\\n}\\n.json-formatter-row .json-formatter-boolean {\\n color: red;\\n}\\n.json-formatter-row .json-formatter-null {\\n color: #855A00;\\n}\\n.json-formatter-row .json-formatter-undefined {\\n color: #ca0b69;\\n}\\n.json-formatter-row .json-formatter-function {\\n color: #FF20ED;\\n}\\n.json-formatter-row .json-formatter-date {\\n background-color: rgba(0, 0, 0, 0.05);\\n}\\n.json-formatter-row .json-formatter-url {\\n text-decoration: underline;\\n color: blue;\\n cursor: pointer;\\n}\\n.json-formatter-row .json-formatter-bracket {\\n color: blue;\\n}\\n.json-formatter-row .json-formatter-key {\\n color: #00008B;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-row .json-formatter-toggler-link {\\n cursor: pointer;\\n}\\n.json-formatter-row .json-formatter-toggler {\\n line-height: 1.2rem;\\n font-size: 0.7rem;\\n vertical-align: middle;\\n opacity: 0.6;\\n cursor: pointer;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-row .json-formatter-toggler:after {\\n display: inline-block;\\n transition: transform 100ms ease-in;\\n content: \\\"\\\\25BA\\\";\\n}\\n.json-formatter-row > a > .json-formatter-preview-text {\\n opacity: 0;\\n transition: opacity 0.15s ease-in;\\n font-style: italic;\\n}\\n.json-formatter-row:hover > a > .json-formatter-preview-text {\\n opacity: 0.6;\\n}\\n.json-formatter-row.json-formatter-open > .json-formatter-toggler-link .json-formatter-toggler:after {\\n transform: rotate(90deg);\\n}\\n.json-formatter-row.json-formatter-open > .json-formatter-children:after {\\n display: inline-block;\\n}\\n.json-formatter-row.json-formatter-open > a > .json-formatter-preview-text {\\n display: none;\\n}\\n.json-formatter-row.json-formatter-open.json-formatter-empty:after {\\n display: block;\\n}\\n.json-formatter-dark.json-formatter-row {\\n font-family: monospace;\\n}\\n.json-formatter-dark.json-formatter-row,\\n.json-formatter-dark.json-formatter-row a,\\n.json-formatter-dark.json-formatter-row a:hover {\\n color: white;\\n text-decoration: none;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-row {\\n margin-left: 1rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty {\\n opacity: 0.5;\\n margin-left: 1rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty:after {\\n display: none;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-object:after {\\n content: \\\"No properties\\\";\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-array:after {\\n content: \\\"[]\\\";\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-string,\\n.json-formatter-dark.json-formatter-row .json-formatter-stringifiable {\\n color: #31F031;\\n white-space: pre;\\n word-wrap: break-word;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-number {\\n color: #66C2FF;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-boolean {\\n color: #EC4242;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-null {\\n color: #EEC97D;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-undefined {\\n color: #ef8fbe;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-function {\\n color: #FD48CB;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-date {\\n background-color: rgba(255, 255, 255, 0.05);\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-url {\\n text-decoration: underline;\\n color: #027BFF;\\n cursor: pointer;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-bracket {\\n color: #9494FF;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-key {\\n color: #23A0DB;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler-link {\\n cursor: pointer;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler {\\n line-height: 1.2rem;\\n font-size: 0.7rem;\\n vertical-align: middle;\\n opacity: 0.6;\\n cursor: pointer;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler:after {\\n display: inline-block;\\n transition: transform 100ms ease-in;\\n content: \\\"\\\\25BA\\\";\\n}\\n.json-formatter-dark.json-formatter-row > a > .json-formatter-preview-text {\\n opacity: 0;\\n transition: opacity 0.15s ease-in;\\n font-style: italic;\\n}\\n.json-formatter-dark.json-formatter-row:hover > a > .json-formatter-preview-text {\\n opacity: 0.6;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > .json-formatter-toggler-link .json-formatter-toggler:after {\\n transform: rotate(90deg);\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > .json-formatter-children:after {\\n display: inline-block;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > a > .json-formatter-preview-text {\\n display: none;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open.json-formatter-empty:after {\\n display: block;\\n}\\n\");\n },\n function(Bokeh) {\n inject_raw_css(\".codehilite .hll { background-color: #ffffcc }\\n.codehilite { background: #f8f8f8; }\\n.codehilite .c { color: #408080; font-style: italic } /* Comment */\\n.codehilite .err { border: 1px solid #FF0000 } /* Error */\\n.codehilite .k { color: #008000; font-weight: bold } /* Keyword */\\n.codehilite .o { color: #666666 } /* Operator */\\n.codehilite .ch { color: #408080; font-style: italic } /* Comment.Hashbang */\\n.codehilite .cm { color: #408080; font-style: italic } /* Comment.Multiline */\\n.codehilite .cp { color: #BC7A00 } /* Comment.Preproc */\\n.codehilite .cpf { color: #408080; font-style: italic } /* Comment.PreprocFile */\\n.codehilite .c1 { color: #408080; font-style: italic } /* Comment.Single */\\n.codehilite .cs { color: #408080; font-style: italic } /* Comment.Special */\\n.codehilite .gd { color: #A00000 } /* Generic.Deleted */\\n.codehilite .ge { font-style: italic } /* Generic.Emph */\\n.codehilite .gr { color: #FF0000 } /* Generic.Error */\\n.codehilite .gh { color: #000080; font-weight: bold } /* Generic.Heading */\\n.codehilite .gi { color: #00A000 } /* Generic.Inserted */\\n.codehilite .go { color: #888888 } /* Generic.Output */\\n.codehilite .gp { color: #000080; font-weight: bold } /* Generic.Prompt */\\n.codehilite .gs { font-weight: bold } /* Generic.Strong */\\n.codehilite .gu { color: #800080; font-weight: bold } /* Generic.Subheading */\\n.codehilite .gt { color: #0044DD } /* Generic.Traceback */\\n.codehilite .kc { color: #008000; font-weight: bold } /* Keyword.Constant */\\n.codehilite .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */\\n.codehilite .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */\\n.codehilite .kp { color: #008000 } /* Keyword.Pseudo */\\n.codehilite .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */\\n.codehilite .kt { color: #B00040 } /* Keyword.Type */\\n.codehilite .m { color: #666666 } /* Literal.Number */\\n.codehilite .s { color: #BA2121 } /* Literal.String */\\n.codehilite .na { color: #7D9029 } /* Name.Attribute */\\n.codehilite .nb { color: #008000 } /* Name.Builtin */\\n.codehilite .nc { color: #0000FF; font-weight: bold } /* Name.Class */\\n.codehilite .no { color: #880000 } /* Name.Constant */\\n.codehilite .nd { color: #AA22FF } /* Name.Decorator */\\n.codehilite .ni { color: #999999; font-weight: bold } /* Name.Entity */\\n.codehilite .ne { color: #D2413A; font-weight: bold } /* Name.Exception */\\n.codehilite .nf { color: #0000FF } /* Name.Function */\\n.codehilite .nl { color: #A0A000 } /* Name.Label */\\n.codehilite .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */\\n.codehilite .nt { color: #008000; font-weight: bold } /* Name.Tag */\\n.codehilite .nv { color: #19177C } /* Name.Variable */\\n.codehilite .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */\\n.codehilite .w { color: #bbbbbb } /* Text.Whitespace */\\n.codehilite .mb { color: #666666 } /* Literal.Number.Bin */\\n.codehilite .mf { color: #666666 } /* Literal.Number.Float */\\n.codehilite .mh { color: #666666 } /* Literal.Number.Hex */\\n.codehilite .mi { color: #666666 } /* Literal.Number.Integer */\\n.codehilite .mo { color: #666666 } /* Literal.Number.Oct */\\n.codehilite .sa { color: #BA2121 } /* Literal.String.Affix */\\n.codehilite .sb { color: #BA2121 } /* Literal.String.Backtick */\\n.codehilite .sc { color: #BA2121 } /* Literal.String.Char */\\n.codehilite .dl { color: #BA2121 } /* Literal.String.Delimiter */\\n.codehilite .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */\\n.codehilite .s2 { color: #BA2121 } /* Literal.String.Double */\\n.codehilite .se { color: #BB6622; font-weight: bold } /* Literal.String.Escape */\\n.codehilite .sh { color: #BA2121 } /* Literal.String.Heredoc */\\n.codehilite .si { color: #BB6688; font-weight: bold } /* Literal.String.Interpol */\\n.codehilite .sx { color: #008000 } /* Literal.String.Other */\\n.codehilite .sr { color: #BB6688 } /* Literal.String.Regex */\\n.codehilite .s1 { color: #BA2121 } /* Literal.String.Single */\\n.codehilite .ss { color: #19177C } /* Literal.String.Symbol */\\n.codehilite .bp { color: #008000 } /* Name.Builtin.Pseudo */\\n.codehilite .fm { color: #0000FF } /* Name.Function.Magic */\\n.codehilite .vc { color: #19177C } /* Name.Variable.Class */\\n.codehilite .vg { color: #19177C } /* Name.Variable.Global */\\n.codehilite .vi { color: #19177C } /* Name.Variable.Instance */\\n.codehilite .vm { color: #19177C } /* Name.Variable.Magic */\\n.codehilite .il { color: #666666 } /* Literal.Number.Integer.Long */\\n\\n.markdown h1 { margin-block-start: 0.34em }\\n.markdown h2 { margin-block-start: 0.42em }\\n.markdown h3 { margin-block-start: 0.5em }\\n.markdown h4 { margin-block-start: 0.67em }\\n.markdown h5 { margin-block-start: 0.84em }\\n.markdown h6 { margin-block-start: 1.17em }\\n.markdown ul { padding-inline-start: 2em }\\n.markdown ol { padding-inline-start: 2em }\\n.markdown strong { font-weight: 600 }\\n.markdown a { color: -webkit-link }\\n.markdown a { color: -moz-hyperlinkText }\\n\");\n },\n function(Bokeh) {\n inject_raw_css(\"table.panel-df {\\n margin-left: auto;\\n margin-right: auto;\\n border: none;\\n border-collapse: collapse;\\n border-spacing: 0;\\n color: black;\\n font-size: 12px;\\n table-layout: fixed;\\n width: 100%;\\n}\\n\\n.panel-df tr, th, td {\\n text-align: right;\\n vertical-align: middle;\\n padding: 0.5em 0.5em !important;\\n line-height: normal;\\n white-space: normal;\\n max-width: none;\\n border: none;\\n}\\n\\n.panel-df tbody {\\n display: table-row-group;\\n vertical-align: middle;\\n border-color: inherit;\\n}\\n\\n.panel-df tbody tr:nth-child(odd) {\\n background: #f5f5f5;\\n}\\n\\n.panel-df thead {\\n border-bottom: 1px solid black;\\n vertical-align: bottom;\\n}\\n\\n.panel-df tr:hover {\\n background: lightblue !important;\\n cursor: pointer;\\n}\\n\");\n },\n function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\n \n function(Bokeh) {\n /* BEGIN panel.min.js */\n /*!\n * Copyright (c) 2012 - 2019, Anaconda, Inc., and Bokeh Contributors\n * All rights reserved.\n * \n * Redistribution and use in source and binary forms, with or without modification,\n * are permitted provided that the following conditions are met:\n * \n * Redistributions of source code must retain the above copyright notice,\n * this list of conditions and the following disclaimer.\n * \n * Redistributions in binary form must reproduce the above copyright notice,\n * this list of conditions and the following disclaimer in the documentation\n * and/or other materials provided with the distribution.\n * \n * Neither the name of Anaconda nor the names of any contributors\n * may be used to endorse or promote products derived from this software\n * without specific prior written permission.\n * \n * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\n * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\n * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE\n * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE\n * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR\n * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF\n * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS\n * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN\n * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)\n * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF\n * THE POSSIBILITY OF SUCH DAMAGE.\n */\n (function(root, factory) {\n factory(root[\"Bokeh\"]);\n })(this, function(Bokeh) {\n var define;\n return (function(modules, entry, aliases, externals) {\n if (Bokeh != null) {\n return Bokeh.register_plugin(modules, entry, aliases, externals);\n } else {\n throw new Error(\"Cannot find Bokeh. You have to load it prior to loading plugins.\");\n }\n })\n ({\n \"aa4f566620\": function _(r,e,t){var n=(this&&this.__importStar||function(r){if(r&&r.__esModule)return r;var e={};if(null!=r)for(var t in r)Object.hasOwnProperty.call(r,t)&&(e[t]=r[t]);return e.default=r,e})(r(\"4d02676c49\"));t.Panel=n,r(\"@bokehjs/base\").register_models(n)},\n \"4d02676c49\": function _(a,e,r){var o=a(\"ff4b91e885\");r.AcePlot=o.AcePlot;var t=a(\"12e90a1b7e\");r.Audio=t.Audio;var c=a(\"cf3b018c7a\");r.DeckGLPlot=c.DeckGLPlot;var d=a(\"70a2bb70ef\");r.HTML=d.HTML;var v=a(\"dac8d750fa\");r.JSON=v.JSON;var P=a(\"c81021c8fd\");r.KaTeX=P.KaTeX;var b=a(\"a93ded647d\");r.MathJax=b.MathJax;var l=a(\"98100899bc\");r.Player=l.Player;var f=a(\"d46f026c83\");r.PlotlyPlot=f.PlotlyPlot;var i=a(\"d9b3a262de\");r.Progress=i.Progress;var n=a(\"4b4afba86a\");r.State=n.State;var S=a(\"14b669e6fc\");r.VegaPlot=S.VegaPlot;var V=a(\"71a2bbec38\");r.Video=V.Video;var s=a(\"76bc93d621\");r.VideoStream=s.VideoStream,function(a){for(var e in a)r.hasOwnProperty(e)||(r[e]=a[e])}(a(\"63070bc9ce\"))},\n \"ff4b91e885\": function _(t,e,o){var i,n=this&&this.__extends||(i=function(t,e){return(i=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var o in e)e.hasOwnProperty(o)&&(t[o]=e[o])})(t,e)},function(t,e){function o(){this.constructor=t}i(t,e),t.prototype=null===e?Object.create(e):(o.prototype=e.prototype,new o)}),r=(this&&this.__importStar||function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var o in t)Object.hasOwnProperty.call(t,o)&&(e[o]=t[o]);return e.default=t,e})(t(\"@bokehjs/core/properties\")),s=t(\"@bokehjs/models/layouts/html_box\"),a=t(\"@bokehjs/core/dom\");var c=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return n(e,t),e.prototype.initialize=function(){t.prototype.initialize.call(this),this._ace=window.ace,this._container=a.div({id:\"_\"+Math.random().toString(36).substr(2,9),style:{width:\"100%\",height:\"100%\"}})},e.prototype.connect_signals=function(){var e=this;t.prototype.connect_signals.call(this),this.connect(this.model.properties.code.change,function(){return e._update_code_from_model()}),this.connect(this.model.properties.theme.change,function(){return e._update_theme()}),this.connect(this.model.properties.language.change,function(){return e._update_language()}),this.connect(this.model.properties.annotations.change,function(){return e._add_annotations()}),this.connect(this.model.properties.readonly.change,function(){e._editor.setReadOnly(e.model.readonly)})},e.prototype.render=function(){var e=this;t.prototype.render.call(this),this._container!==this.el.childNodes[0]&&this.el.appendChild(this._container),this._container.textContent=this.model.code,this._editor=this._ace.edit(this._container.id),this._editor.setTheme(\"ace/theme/\"+this.model.theme),this._editor.session.setMode(\"ace/mode/\"+this.model.language),this._editor.setReadOnly(this.model.readonly),this._langTools=this._ace.require(\"ace/ext/language_tools\"),this._editor.setOptions({enableBasicAutocompletion:!0,enableSnippets:!0,fontFamily:\"monospace\"}),this._editor.on(\"change\",function(){return e._update_code_from_editor()})},e.prototype._update_code_from_model=function(){this._editor&&this._editor.getValue()!=this.model.code&&this._editor.setValue(this.model.code)},e.prototype._update_code_from_editor=function(){this._editor.getValue()!=this.model.code&&(this.model.code=this._editor.getValue())},e.prototype._update_theme=function(){this._editor.setTheme(\"ace/theme/\"+this.model.theme)},e.prototype._update_language=function(){this._editor.session.setMode(\"ace/mode/\"+this.model.language)},e.prototype._add_annotations=function(){this._editor.session.setAnnotations(this.model.annotations)},e.prototype.after_layout=function(){t.prototype.after_layout.call(this),this._editor.resize()},e.__name__=\"AcePlotView\",e}(t(\"ec60963462\").PanelHTMLBoxView);o.AcePlotView=c;var h=function(t){function e(e){return t.call(this,e)||this}return n(e,t),e.init_AcePlot=function(){this.prototype.default_view=c,this.define({code:[r.String],language:[r.String,\"python\"],theme:[r.String,\"chrome\"],annotations:[r.Array,[]],readonly:[r.Boolean,!1]}),this.override({height:300,width:300})},e.__name__=\"AcePlot\",e.__module__=\"panel.models.ace\",e}(s.HTMLBox);o.AcePlot=h,h.init_AcePlot()},\n \"ec60963462\": function _(e,t,i){var o,n=this&&this.__extends||(o=function(e,t){return(o=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(e,t){e.__proto__=t}||function(e,t){for(var i in t)t.hasOwnProperty(i)&&(e[i]=t[i])})(e,t)},function(e,t){function i(){this.constructor=e}o(e,t),e.prototype=null===t?Object.create(t):(i.prototype=t.prototype,new i)}),s=e(\"@bokehjs/core/layout/layoutable\"),h=e(\"@bokehjs/core/layout/types\"),r=e(\"@bokehjs/core/dom\"),a=e(\"@bokehjs/models/widgets/markup\"),_=e(\"@bokehjs/models/layouts/html_box\");function c(e,t){var i=null!=t.width?\"fixed\":\"fit\",o=null!=t.height?\"fixed\":\"fit\",n=t.sizing_mode;if(null!=n)if(\"fixed\"==n)i=o=\"fixed\";else if(\"stretch_both\"==n)i=o=\"max\";else if(\"stretch_width\"==n)i=\"max\";else if(\"stretch_height\"==n)o=\"max\";else switch(n){case\"scale_width\":i=\"max\",o=\"min\";break;case\"scale_height\":i=\"min\",o=\"max\";break;case\"scale_both\":i=\"max\",o=\"max\";break;default:throw new Error(\"unreachable\")}\"fixed\"==i&&t.width?e.style.width=t.width+\"px\":\"max\"==i&&(e.style.width=\"100%\"),\"fixed\"==o&&t.height?e.style.height=t.height+\"px\":\"max\"==o&&(e.style.height=\"100%\")}i.set_size=c;var l=function(e){function t(t,i,o){var n=e.call(this)||this;return n.el=t,n.sizing_mode=i,n.changed=o,n._cache={},n._cache_count={},n}return n(t,e),t.prototype._measure=function(e){var t=this,i=[e.width,e.height,this.sizing_mode].toString(),o=this.changed&&\"fixed\"!=this.sizing_mode&&null!=this.sizing_mode?1:0;if(i in this._cache&&this._cache_count[i]>=o)return this._cache_count[i]=this._cache_count[i]+1,this._cache[i];var n=new h.Sizeable(e).bounded_to(this.sizing.size),s=r.sized(this.el,n,function(){var e=new h.Sizeable(r.content_size(t.el)),i=r.extents(t.el),o=i.border,n=i.padding;return e.grow_by(o).grow_by(n).map(Math.ceil)});return this._cache[i]=s,this._cache_count[i]=0,s},t.__name__=\"CachedVariadicBox\",t}(s.Layoutable);i.CachedVariadicBox=l;var d=function(e){function t(){return null!==e&&e.apply(this,arguments)||this}return n(t,e),t.prototype._update_layout=function(){var e=void 0!==this._prev_sizing_mode&&this._prev_sizing_mode!==this.model.sizing_mode;this._prev_sizing_mode=this.model.sizing_mode,this.layout=new l(this.el,this.model.sizing_mode,e),this.layout.set_sizing(this.box_sizing())},t.prototype.render=function(){e.prototype.render.call(this),c(this.markup_el,this.model)},t.__name__=\"PanelMarkupView\",t}(a.MarkupView);i.PanelMarkupView=d;var u=function(e){function t(){return null!==e&&e.apply(this,arguments)||this}return n(t,e),t.prototype._update_layout=function(){var e=void 0!==this._prev_sizing_mode&&this._prev_sizing_mode!==this.model.sizing_mode;this._prev_sizing_mode=this.model.sizing_mode,this.layout=new l(this.el,this.model.sizing_mode,e),this.layout.set_sizing(this.box_sizing())},t.prototype.render=function(){e.prototype.render.call(this),c(this.el,this.model)},t.__name__=\"PanelHTMLBoxView\",t}(_.HTMLBoxView);i.PanelHTMLBoxView=u},\n \"12e90a1b7e\": function _(t,e,o){var i,n=this&&this.__extends||(i=function(t,e){return(i=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var o in e)e.hasOwnProperty(o)&&(t[o]=e[o])})(t,e)},function(t,e){function o(){this.constructor=t}i(t,e),t.prototype=null===e?Object.create(e):(o.prototype=e.prototype,new o)}),u=(this&&this.__importStar||function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var o in t)Object.hasOwnProperty.call(t,o)&&(e[o]=t[o]);return e.default=t,e})(t(\"@bokehjs/core/properties\")),l=t(\"@bokehjs/models/layouts/html_box\"),s=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return n(e,t),e.prototype.initialize=function(){t.prototype.initialize.call(this),this._blocked=!1,this._setting=!1,this._time=Date.now()},e.prototype.connect_signals=function(){var e=this;t.prototype.connect_signals.call(this),this.connect(this.model.properties.loop.change,function(){return e.set_loop()}),this.connect(this.model.properties.paused.change,function(){return e.set_paused()}),this.connect(this.model.properties.time.change,function(){return e.set_time()}),this.connect(this.model.properties.value.change,function(){return e.set_value()}),this.connect(this.model.properties.volume.change,function(){return e.set_volume()})},e.prototype.render=function(){var e=this;t.prototype.render.call(this),this.audioEl=document.createElement(\"audio\"),this.audioEl.controls=!0,this.audioEl.src=this.model.value,this.audioEl.currentTime=this.model.time,this.audioEl.loop=this.model.loop,null!=this.model.volume?this.audioEl.volume=this.model.volume/100:this.model.volume=100*this.audioEl.volume,this.audioEl.onpause=function(){return e.model.paused=!0},this.audioEl.onplay=function(){return e.model.paused=!1},this.audioEl.ontimeupdate=function(){return e.update_time(e)},this.audioEl.onvolumechange=function(){return e.update_volume(e)},this.el.appendChild(this.audioEl),this.model.paused||this.audioEl.play()},e.prototype.update_time=function(t){t._setting?t._setting=!1:Date.now()-t._time1&&\"number\"==typeof h[0]?l[u]=r.data[u].slice(c*h[1],c*h[1]+h[1]):l[u]=r.data[u][c]}a.push(l)}i.data=a}t&&this.updateDeck()},e.prototype._on_click_event=function(t){var e={coordinate:t.coordinate,lngLat:t.lngLat,index:t.index};this.model.clickState=e},e.prototype._on_hover_event=function(t){var e={coordinate:t.coordinate,lngLat:t.lngLat,index:t.index};this.model.hoverState=e},e.prototype._on_viewState_event=function(t){this.model.viewState=t.viewState},e.prototype.getData=function(){var t=this;return r(r({},this.model.data),{layers:this.model.layers,initialViewState:this.model.initialViewState,onViewStateChange:function(e){return t._on_viewState_event(e)},onClick:function(e){return t._on_click_event(e)},onHover:function(e){return t._on_hover_event(e)}})},e.prototype.updateDeck=function(){if(this.deckGL){var t=this.getData();if(d.updateDeck)d.updateDeck(t,this.deckGL);else{var e=this.jsonConverter.convert(t);this.deckGL.setProps(e)}}else this.render()},e.prototype.createDeck=function(t){var e,o=t.mapboxApiKey,n=t.container,i=t.jsonInput,a=t.tooltip;try{var s=this.jsonConverter.convert(i),c=u.makeTooltip(a);e=new d.DeckGL(r(r({},s),{map:f,mapboxApiAccessToken:o,container:n,getTooltip:c}))}catch(t){console.error(t)}return e},e.prototype.render=function(){t.prototype.render.call(this);var e=c.div({class:\"deckgl\"});_.set_size(e,this.model);var o=this.model.mapbox_api_key,n=this.model.tooltip,i=this.getData();d.createDeck?this.deckGL=d.createDeck({mapboxApiKey:o,container:e,jsonInput:i,tooltip:n}):this.deckGL=this.createDeck({mapboxApiKey:o,container:e,jsonInput:i,tooltip:n}),this.el.appendChild(e)},e.__name__=\"DeckGLPlotView\",e}(_.PanelHTMLBoxView);o.DeckGLPlotView=m;var k=function(t){function e(e){return t.call(this,e)||this}return i(e,t),e.init_DeckGLPlot=function(){this.prototype.default_view=m,this.define({data:[l.Any],data_sources:[l.Array,[]],clickState:[l.Any],hoverState:[l.Any],initialViewState:[l.Any],layers:[l.Array,[]],mapbox_api_key:[l.String],tooltip:[l.Any],viewState:[l.Any]}),this.override({height:400,width:600})},e.__name__=\"DeckGLPlot\",e.__module__=\"panel.models.deckgl\",e}(p.HTMLBox);o.DeckGLPlot=k,k.init_DeckGLPlot()},\n \"27d3545a25\": function _(e,t,n){var i,r,l={fontFamily:'\"Helvetica Neue\", Helvetica, Arial, sans-serif',display:\"flex\",flex:\"wrap\",maxWidth:\"500px\",flexDirection:\"column\",zIndex:2};function a(){return document.createElement(\"div\")}function o(e){if(!e.picked)return null;if(e.object===i)return r;var t={html:c(e.object),style:l};return r=t,i=e.object,t}n.getTooltipDefault=o;var s=new Set([\"position\",\"index\"]);function c(e){var t=a();for(var n in e)if(!s.has(n)){var i=a();i.className=\"header\",i.textContent=n;var r=a();r.className=\"value\",r.textContent=u(e[n]);var l=a();f(l,i,r),l.appendChild(i),l.appendChild(r),t.appendChild(l)}return t.innerHTML}function f(e,t,n){Object.assign(t.style,{fontWeight:700,marginRight:\"10px\",flex:\"1 1 0%\"}),Object.assign(n.style,{flex:\"none\",maxWidth:\"250px\",overflow:\"hidden\",whiteSpace:\"nowrap\",textOverflow:\"ellipsis\"}),Object.assign(e.style,{display:\"flex\",flexDirection:\"row\",justifyContent:\"space-between\",alignItems:\"stretch\"})}function u(e){var t;if(Array.isArray(e)&&e.length>4)t=\"Array<\"+e.length+\">\";else if(\"string\"==typeof e)t=e;else if(\"number\"==typeof e)t=String(e);else try{t=JSON.stringify(e)}catch(e){t=\"\"}return t.length>50&&(t=t.slice(0,50)),t}function p(e,t){var n=e;for(var i in t)n=n.replace(\"{\"+i+\"}\",t[i]);return n}n.tabularize=c,n.toText=u,n.substituteIn=p,n.makeTooltip=function(e){return e?e.html||e.text?function(t){if(!t.picked)return null;var n={style:e.style||l};return 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user-select:none;\",\"once\"==this.model.loop_policy?m.checked=!0:\"loop\"==this.model.loop_policy?f.checked=!0:y.checked=!0,this.loop_state.appendChild(m),this.loop_state.appendChild(_),this.loop_state.appendChild(f),this.loop_state.appendChild(v),this.loop_state.appendChild(y),this.loop_state.appendChild(x),this.el.appendChild(this.sliderEl),this.el.appendChild(i),this.el.appendChild(this.loop_state)},e.prototype.set_frame=function(t){this.model.value!=t&&(this.model.value=t),this.sliderEl.value!=String(t)&&(this.sliderEl.value=String(t))},e.prototype.get_loop_state=function(){for(var t=this.loop_state.state,e=0;e0?this.play_animation():this.model.direction<0&&this.reverse_animation()},e.prototype.faster=function(){this.model.interval=Math.round(.7*this.model.interval),this.model.direction>0?this.play_animation():this.model.direction<0&&this.reverse_animation()},e.prototype.anim_step_forward=function(){if(this.model.valuethis.model.start)this.previous_frame();else{var t=this.get_loop_state();\"loop\"==t?this.last_frame():\"reflect\"==t?(this.first_frame(),this.play_animation()):(this.pause_animation(),this.first_frame())}},e.prototype.pause_animation=function(){this.model.direction=0,this.timer&&(clearInterval(this.timer),this.timer=null)},e.prototype.play_animation=function(){var t=this;this.pause_animation(),this.model.direction=1,this.timer||(this.timer=setInterval(function(){return t.anim_step_forward()},this.model.interval))},e.prototype.reverse_animation=function(){var t=this;this.pause_animation(),this.model.direction=-1,this.timer||(this.timer=setInterval(function(){return t.anim_step_reverse()},this.model.interval))},e.__name__=\"PlayerView\",e}(a.WidgetView);i.PlayerView=l;var d=function(t){function e(e){return t.call(this,e)||this}return o(e,t),e.init_Player=function(){this.prototype.default_view=l,this.define({direction:[r.Number,0],interval:[r.Number,500],start:[r.Number],end:[r.Number],step:[r.Number,1],loop_policy:[r.Any,\"once\"],value:[r.Any,0]}),this.override({width:400})},e.__name__=\"Player\",e.__module__=\"panel.models.widgets\",e}(a.Widget);i.Player=d,d.init_Player()},\n \"d46f026c83\": function _(t,e,o){var r,n=this&&this.__extends||(r=function(t,e){return(r=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var o in e)e.hasOwnProperty(o)&&(t[o]=e[o])})(t,e)},function(t,e){function o(){this.constructor=t}r(t,e),t.prototype=null===e?Object.create(e):(o.prototype=e.prototype,new o)}),i=(this&&this.__importStar||function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var o in t)Object.hasOwnProperty.call(t,o)&&(e[o]=t[o]);return e.default=t,e})(t(\"@bokehjs/core/properties\")),l=t(\"@bokehjs/core/util/object\"),a=t(\"@bokehjs/core/util/eq\"),p=t(\"@bokehjs/models/layouts/html_box\"),s=t(\"99a25e6992\"),u=t(\"62ba79515f\"),c=t(\"ec60963462\"),_=window.Plotly,d=function(t,e,o){var r=Array.isArray(e)?[]:{};if(\"click\"===o||\"hover\"===o||\"selected\"===o){var n=[];if(null==e)return null;for(var i=t.data,l=0;l1){for(var u=[],c=0;c=0?t=setTimeout(i,l-c):(t=null,u||(r=n.apply(o,e),o=e=null))}null==l&&(l=100);var c=function(){o=this,e=arguments,a=Date.now();var c=u&&!t;return t||(t=setTimeout(i,l)),c&&(r=n.apply(o,e),o=e=null),r};return c.clear=function(){t&&(clearTimeout(t),t=null)},c.flush=function(){t&&(r=n.apply(o,e),o=e=null,clearTimeout(t),t=null)},c}t.debounce=t,l.exports=t},\n \"62ba79515f\": function _(t,r,n){n.get=function(t,r,n){void 0===n&&(n=void 0);var e=function(n){return String.prototype.split.call(r,n).filter(Boolean).reduce(function(t,r){return null!=t?t[r]:t},t)},o=e(/[,[\\]]+?/)||e(/[,[\\].]+?/);return void 0===o||o===t?n:o},n.throttle=function(t,r){var n=0;return function(){var e=Number(new Date);e-n>=r&&(t(),n=e)}},n.deepCopy=function t(r){var n;if(null==r||\"object\"!=typeof r)return r;if(r instanceof Array){n=[];for(var e=0,o=r.length;e0){var t=this._fetch_datasets();if(\"data\"in t&&(this.model.data.data.values=t.data,delete t.data),void 0!==this.model.data.data)for(var e=0,o=this.model.data.data;e0&&(this.timer=setInterval(function(){return t.snapshot()},this.model.timeout))},e.prototype.snapshot=function(){this.canvasEl.width=this.videoEl.videoWidth,this.canvasEl.height=this.videoEl.videoHeight;var t=this.canvasEl.getContext(\"2d\");t&&t.drawImage(this.videoEl,0,0,this.canvasEl.width,this.canvasEl.height),this.model.value=this.canvasEl.toDataURL(\"image/\"+this.model.format,.95)},e.prototype.remove=function(){t.prototype.remove.call(this),this.timer&&(clearInterval(this.timer),this.timer=null)},e.prototype.render=function(){var e=this;t.prototype.render.call(this),this.videoEl||(this.videoEl=document.createElement(\"video\"),this.model.sizing_mode&&\"fixed\"!==this.model.sizing_mode||(this.model.height&&(this.videoEl.height=this.model.height),this.model.width&&(this.videoEl.width=this.model.width)),this.videoEl.style.objectFit=\"fill\",this.videoEl.style.minWidth=\"100%\",this.videoEl.style.minHeight=\"100%\",this.canvasEl=document.createElement(\"canvas\"),this.el.appendChild(this.videoEl),navigator.mediaDevices.getUserMedia&&navigator.mediaDevices.getUserMedia(this.constraints).then(function(t){e.videoEl.srcObject=t,e.model.paused||e.videoEl.play()}).catch(console.error))},e.__name__=\"VideoStreamView\",e}(t(\"ec60963462\").PanelHTMLBoxView);i.VideoStreamView=h;var a=function(t){function e(e){return t.call(this,e)||this}return n(e,t),e.init_VideoStream=function(){this.prototype.default_view=h,this.define({format:[s.String,\"png\"],paused:[s.Boolean,!1],snapshot:[s.Boolean,!1],timeout:[s.Number,0],value:[s.Any]}),this.override({height:240,width:320})},e.__name__=\"VideoStream\",e.__module__=\"panel.models.widgets\",e}(r.HTMLBox);i.VideoStream=a,a.init_VideoStream()},\n \"63070bc9ce\": function _(V,o,e){var l=V(\"1a4b530306\");e.VTKPlot=l.VTKPlot;var K=V(\"b933e81f56\");e.VTKVolumePlot=K.VTKVolumePlot;var T=V(\"5bc27423fe\");e.VTKAxes=T.VTKAxes},\n \"1a4b530306\": function _(e,t,n){var i,o=this&&this.__extends||(i=function(e,t){return(i=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(e,t){e.__proto__=t}||function(e,t){for(var n in t)t.hasOwnProperty(n)&&(e[n]=t[n])})(e,t)},function(e,t){function n(){this.constructor=e}i(e,t),e.prototype=null===t?Object.create(t):(n.prototype=t.prototype,new n)}),r=(this&&this.__importStar||function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t})(e(\"@bokehjs/core/properties\")),a=e(\"@bokehjs/core/dom\"),s=e(\"7620c2cc05\"),c=e(\"3b847a648d\"),d=function(e){function t(){var t=null!==e&&e.apply(this,arguments)||this;return t._axes_initialized=!1,t}return o(t,e),t.prototype.connect_signals=function(){var t=this;e.prototype.connect_signals.call(this),this.connect(this.model.properties.axes.change,function(){t._delete_axes(),t.model.axes&&t._set_axes(),t._vtk_renwin.getRenderWindow().render()}),this.el.addEventListener(\"mouseenter\",function(){var e=t._vtk_renwin.getInteractor();t.model.enable_keybindings&&(document.querySelector(\"body\").addEventListener(\"keypress\",e.handleKeyPress),document.querySelector(\"body\").addEventListener(\"keydown\",e.handleKeyDown),document.querySelector(\"body\").addEventListener(\"keyup\",e.handleKeyUp))}),this.el.addEventListener(\"mouseleave\",function(){var e=t._vtk_renwin.getInteractor();document.querySelector(\"body\").removeEventListener(\"keypress\",e.handleKeyPress),document.querySelector(\"body\").removeEventListener(\"keydown\",e.handleKeyDown),document.querySelector(\"body\").removeEventListener(\"keyup\",e.handleKeyUp)})},t.prototype.render=function(){e.prototype.render.call(this),this._axes=null,this._axes_initialized=!1,this._plot()},t.prototype.after_layout=function(){this._axes_initialized||(this._render_axes_canvas(),this._axes_initialized=!0)},t.prototype._render_axes_canvas=function(){var e=this,t=this._vtk_container.getElementsByTagName(\"canvas\");if(1!=t.length)throw Error(\"Error at initialization of the 3D scene, container should have one and only one canvas\");t[0].classList.add(\"scene3d-canvas\");var n=a.canvas({style:{position:\"absolute\",top:\"0\",left:\"0\",width:\"100%\",height:\"100%\"}});n.classList.add(\"axes-canvas\"),this._vtk_container.appendChild(n),this._vtk_renwin.setResizeCallback(function(){var t=e._vtk_container.getBoundingClientRect(),i=Math.floor(t.width*window.devicePixelRatio),o=Math.floor(t.height*window.devicePixelRatio);n.setAttribute(\"width\",i.toFixed()),n.setAttribute(\"height\",o.toFixed())})},t.prototype._delete_axes=function(){var e=this;if(null!=this._axes){Object.keys(this._axes).forEach(function(t){return e._vtk_renwin.getRenderer().removeActor(e._axes[t])});var t=this._vtk_renwin.getContainer().getElementsByClassName(\"axes-canvas\")[0],n=t.getContext(\"2d\");n&&n.clearRect(0,0,t.clientWidth*window.devicePixelRatio,t.clientHeight*window.devicePixelRatio),this._axes=null}},t.prototype._set_axes=function(){if(this.model.axes){var e=this._vtk_renwin.getContainer().getElementsByClassName(\"axes-canvas\")[0],t=this.model.axes.create_axes(e),n=t.psActor,i=t.axesActor,o=t.gridActor;this._axes={psActor:n,axesActor:i,gridActor:o},this._vtk_renwin.getRenderer().addActor(n),this._vtk_renwin.getRenderer().addActor(i),this._vtk_renwin.getRenderer().addActor(o)}},t.prototype._plot=function(){var e=this;if(this.model.data)var t=c.vtkns.DataAccessHelper.get(\"zip\",{zipContent:atob(this.model.data),callback:function(n){var i=c.vtkns.HttpSceneLoader.newInstance({renderer:e._vtk_renwin.getRenderer(),dataAccessHelper:t}),o=c.vtk.macro.debounce(function(){null==e._axes&&e.model.axes&&e._set_axes(),e.model.properties.camera.change.emit()},100);i.setUrl(\"index.json\"),i.onReady(o)}});else this._vtk_renwin.getRenderWindow().render()},t.__name__=\"VTKPlotView\",t}(s.AbstractVTKView);n.VTKPlotView=d;var l=function(e){function t(t){var n=e.call(this,t)||this;n.outline=c.vtkns.OutlineFilter.newInstance();var i=c.vtkns.Mapper.newInstance();return i.setInputConnection(n.outline.getOutputPort()),n.outline_actor=c.vtkns.Actor.newInstance(),n.outline_actor.setMapper(i),n}return o(t,e),t.init_VTKPlot=function(){this.prototype.default_view=d,this.define({data:[r.String],axes:[r.Instance],enable_keybindings:[r.Boolean,!1]})},t.__name__=\"VTKPlot\",t}(s.AbstractVTKPlot);n.VTKPlot=l,l.init_VTKPlot()},\n \"7620c2cc05\": function _(e,t,n){var i,r=this&&this.__extends||(i=function(e,t){return(i=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(e,t){e.__proto__=t}||function(e,t){for(var n in t)t.hasOwnProperty(n)&&(e[n]=t[n])})(e,t)},function(e,t){function n(){this.constructor=e}i(e,t),e.prototype=null===t?Object.create(t):(n.prototype=t.prototype,new n)}),o=(this&&this.__importStar||function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t})(e(\"@bokehjs/core/properties\")),a=e(\"@bokehjs/core/dom\"),s=e(\"@bokehjs/core/util/object\"),_=e(\"@bokehjs/models/layouts/html_box\"),c=e(\"ec60963462\"),d=e(\"3b847a648d\"),h=function(e){function t(){var t=null!==e&&e.apply(this,arguments)||this;return t._setting_camera=!1,t}return r(t,e),t.prototype.connect_signals=function(){var t=this;e.prototype.connect_signals.call(this),this.connect(this.model.properties.data.change,function(){t.invalidate_render()}),this.connect(this.model.properties.orientation_widget.change,function(){t._orientation_widget_visibility(t.model.orientation_widget)}),this.connect(this.model.properties.camera.change,function(){return t._set_camera_state()})},t.prototype._orientation_widget_visibility=function(e){this._orientationWidget.setEnabled(e),e?this._widgetManager.enablePicking():this._widgetManager.disablePicking(),this._orientationWidget.updateMarkerOrientation(),this._vtk_renwin.getRenderWindow().render()},t.prototype._create_orientation_widget=function(){var e=this,t=d.vtkns.AxesActor.newInstance(),n=d.vtkns.OrientationMarkerWidget.newInstance({actor:t,interactor:this._vtk_renwin.getInteractor()});n.setEnabled(!0),n.setViewportCorner(d.vtkns.OrientationMarkerWidget.Corners.BOTTOM_RIGHT),n.setViewportSize(.15),n.setMinPixelSize(100),n.setMaxPixelSize(300),this._orientationWidget=n;var i=d.vtkns.WidgetManager.newInstance();i.setRenderer(n.getRenderer());var r=d.vtkns.InteractiveOrientationWidget.newInstance();r.placeWidget(t.getBounds()),r.setBounds(t.getBounds()),r.setPlaceFactor(1);var o=i.addWidget(r);this._widgetManager=i,o.onOrientationChange(function(t){var n=t.direction,i=e._vtk_renwin.getRenderer().getActiveCamera(),r=i.getFocalPoint(),o=i.getPosition(),a=i.getViewUp(),s=Math.sqrt(Math.pow(o[0]-r[0],2)+Math.pow(o[1]-r[1],2)+Math.pow(o[2]-r[2],2));i.setPosition(r[0]+n[0]*s,r[1]+n[1]*s,r[2]+n[2]*s),n[0]&&i.setViewUp(d.majorAxis(a,1,2)),n[1]&&i.setViewUp(d.majorAxis(a,0,2)),n[2]&&i.setViewUp(d.majorAxis(a,0,1)),e._orientationWidget.updateMarkerOrientation(),e._vtk_renwin.getRenderer().resetCameraClippingRange(),e._vtk_renwin.getRenderWindow().render()}),this._orientation_widget_visibility(this.model.orientation_widget)},t.prototype._get_camera_state=function(){if(!this._setting_camera){this._setting_camera=!0;var e=s.clone(this._vtk_renwin.getRenderer().getActiveCamera().get());delete e.classHierarchy,delete e.vtkObject,delete e.vtkCamera,delete e.viewPlaneNormal,this.model.camera=e,this._setting_camera=!1}},t.prototype._set_camera_state=function(){if(!this._setting_camera){this._setting_camera=!0;try{this.model.camera&&this._vtk_renwin.getRenderer().getActiveCamera().set(this.model.camera)}finally{this._setting_camera=!1}this._orientationWidget.updateMarkerOrientation(),this._vtk_renwin.getRenderer().resetCameraClippingRange(),this._vtk_renwin.getRenderWindow().render()}},t.prototype.render=function(){var t=this;e.prototype.render.call(this),this._orientationWidget=null,this._vtk_container=a.div(),c.set_size(this._vtk_container,this.model),this.el.appendChild(this._vtk_container),this._vtk_renwin=d.vtkns.FullScreenRenderWindow.newInstance({rootContainer:this.el,container:this._vtk_container}),this._remove_default_key_binding(),this._create_orientation_widget(),this._vtk_renwin.getRenderer().getActiveCamera().onModified(function(){return t._get_camera_state()}),this._set_camera_state(),this.model.renderer_el=this._vtk_renwin},t.prototype.after_layout=function(){e.prototype.after_layout.call(this),this._vtk_renwin.resize()},t.prototype._remove_default_key_binding=function(){var e=this._vtk_renwin.getInteractor();document.querySelector(\"body\").removeEventListener(\"keypress\",e.handleKeyPress),document.querySelector(\"body\").removeEventListener(\"keydown\",e.handleKeyDown),document.querySelector(\"body\").removeEventListener(\"keyup\",e.handleKeyUp)},t.__name__=\"AbstractVTKView\",t}(c.PanelHTMLBoxView);n.AbstractVTKView=h;var l=function(e){function t(t){return e.call(this,t)||this}return r(t,e),t.prototype.getActors=function(){return this.renderer_el.getRenderer().getActors()},t.init_AbstractVTKPlot=function(){this.define({orientation_widget:[o.Boolean,!1],camera:[o.Instance]}),this.override({height:300,width:300})},t.__name__=\"AbstractVTKPlot\",t.__module__=\"panel.models.vtk\",t}(_.HTMLBox);n.AbstractVTKPlot=l,l.init_AbstractVTKPlot()},\n \"3b847a648d\": function _(e,t,n){var r=e(\"@bokehjs/core/util/serialization\"),a=e(\"@bokehjs/core/util/array\");function o(e){var t=Math.min(Math.max(Math.round(e),0),255).toString(16);return 2==t.length?t:\"0\"+t}function i(e,t,n){return\"#\"+o(e)+o(t)+o(n)}function v(e){for(var t=new ArrayBuffer(e.length),n=new Uint8Array(t),r=0,a=e.length;rMath.abs(e[n])?t:n,o=e[a]>0?1:-1;return r[a]=o,r},n.cartesian_product=function(){for(var e=[],t=0;t=.005&&(e.model.sampling=t)}),Math.abs(this.model.sampling-Number(this.shadow_selector.value))>=.005&&this.model.properties.sampling.change.emit(),this.edge_gradient_slider.addEventListener(\"input\",function(){var t=Number(e.edge_gradient_slider.value);Math.abs(e.model.edge_gradient-t)>=.005&&(e.model.edge_gradient=t)}),Math.abs(this.model.edge_gradient-Number(this.edge_gradient_slider.value))>=.005&&this.model.properties.edge_gradient.change.emit()},t.prototype._plot_volume=function(){var e=this,t=this._vtk_image_data,n=a.vtkns.Volume.newInstance(),r=a.vtkns.VolumeMapper.newInstance();n.setMapper(r),r.setInputData(t);var i=(t.getPointData().getScalars()||t.getPointData().getArrays()[0]).getRange(),o=a.vtkns.ColorTransferFunction.newInstance();o.onModified(function(){return e.model.mapper=a.vtkLutToMapper(o)});var s=a.vtkns.PiecewiseFunction.newInstance(),l=.7*Math.sqrt(t.getSpacing().map(function(e){return e*e}).reduce(function(e,t){return e+t},0));r.setSampleDistance(l),n.getProperty().setRGBTransferFunction(0,o),n.getProperty().setScalarOpacity(0,s),n.getProperty().setInterpolationTypeToFastLinear(),n.getProperty().setScalarOpacityUnitDistance(0,a.vtkns.BoundingBox.getDiagonalLength(t.getBounds())/Math.max.apply(Math,t.getDimensions())),n.getProperty().setGradientOpacityMinimumValue(0,0),n.getProperty().setGradientOpacityMaximumValue(0,.05*(i[1]-i[0])),n.getProperty().setShade(this.model.shadow),n.getProperty().setUseGradientOpacity(0,!0),n.getProperty().setGradientOpacityMinimumOpacity(0,0),n.getProperty().setGradientOpacityMaximumOpacity(0,1),n.getProperty().setAmbient(this.model.ambient),n.getProperty().setDiffuse(this.model.diffuse),n.getProperty().setSpecular(this.model.specular),n.getProperty().setSpecularPower(this.model.specular_power),this._vtk_renwin.getRenderer().addVolume(n),this._controllerWidget.setupContent(this._vtk_renwin.getRenderWindow(),n,!0)},t.prototype._plot_slices=function(){var e=this._vtk_image_data,t=a.vtkns.ImageSlice.newInstance(),n=a.vtkns.ImageSlice.newInstance(),r=a.vtkns.ImageSlice.newInstance(),i=a.vtkns.ImageMapper.newInstance(),o=a.vtkns.ImageMapper.newInstance(),s=a.vtkns.ImageMapper.newInstance();i.setInputData(e),i.setISlice(this.model.slice_i),t.setMapper(i),o.setInputData(e),o.setJSlice(this.model.slice_j),n.setMapper(o),s.setInputData(e),s.setKSlice(this.model.slice_k),r.setMapper(s);var l=a.vtkns.PiecewiseFunction.newInstance();l.removeAllPoints(),l.addPoint(0,1);var c=this.volume.getProperty().getRGBTransferFunction(0),p=t.getProperty();n.setProperty(p),r.setProperty(p),p.setRGBTransferFunction(c),p.setScalarOpacity(l);var d=this._vtk_renwin.getRenderer();d.addActor(t),d.addActor(n),d.addActor(r)},t.prototype._set_volume_visibility=function(e){this.volume.setVisibility(e)},t.prototype._set_slices_visibility=function(e){this._vtk_renwin.getRenderer().getActors().map(function(t){return t.setVisibility(e)})},t.__name__=\"VTKVolumePlotView\",t}(s.AbstractVTKView);n.VTKVolumePlotView=l;var c=function(e){function t(t){return e.call(this,t)||this}return i(t,e),t.init_VTKVolumePlot=function(){this.prototype.default_view=l,this.define({data:[o.Instance],shadow:[o.Boolean,!0],sampling:[o.Number,.4],edge_gradient:[o.Number,.2],colormap:[o.String],rescale:[o.Boolean,!1],ambient:[o.Number,.2],diffuse:[o.Number,.7],specular:[o.Number,.3],specular_power:[o.Number,8],slice_i:[o.Int,0],slice_j:[o.Int,0],slice_k:[o.Int,0],display_volume:[o.Boolean,!0],display_slices:[o.Boolean,!1],render_background:[o.String,\"#52576e\"],interpolation:[o.Any,\"fast_linear\"],mapper:[o.Instance]})},t.__name__=\"VTKVolumePlot\",t}(s.AbstractVTKPlot);n.VTKVolumePlot=c,c.init_VTKVolumePlot()},\n \"5bc27423fe\": function _(t,e,i){var s,n=this&&this.__extends||(s=function(t,e){return(s=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var i in 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t[0]=(1-(l+m))*S,t[1]=(c+P)*S,t[2]=(b-y)*S,t[3]=0,t[4]=(c-P)*O,t[5]=(1-(f+m))*O,t[6]=(v+p)*O,t[7]=0,t[8]=(b+y)*E,t[9]=(v-p)*E,t[10]=(1-(f+l))*E,t[11]=0,t[12]=n[0],t[13]=n[1],t[14]=n[2],t[15]=1,t},n.fromRotationTranslationScaleOrigin=function(t,a,n,r,o){var e=a[0],u=a[1],h=a[2],i=a[3],M=e+e,s=u+u,f=h+h,c=e*M,b=e*s,l=e*f,v=u*s,m=u*f,p=h*f,y=i*M,P=i*s,S=i*f,O=r[0],E=r[1],I=r[2],L=o[0],N=o[1],R=o[2],x=(1-(v+p))*O,d=(b+S)*O,g=(l-P)*O,A=(b-S)*E,Y=(1-(c+p))*E,T=(m+y)*E,w=(l+P)*I,_=(m-y)*I,q=(1-(c+v))*I;return t[0]=x,t[1]=d,t[2]=g,t[3]=0,t[4]=A,t[5]=Y,t[6]=T,t[7]=0,t[8]=w,t[9]=_,t[10]=q,t[11]=0,t[12]=n[0]+L-(x*L+A*N+w*R),t[13]=n[1]+N-(d*L+Y*N+_*R),t[14]=n[2]+R-(g*L+T*N+q*R),t[15]=1,t},n.fromQuat=function(t,a){var n=a[0],r=a[1],o=a[2],e=a[3],u=n+n,h=r+r,i=o+o,M=n*u,s=r*u,f=r*h,c=o*u,b=o*h,l=o*i,v=e*u,m=e*h,p=e*i;return t[0]=1-f-l,t[1]=s+p,t[2]=c-m,t[3]=0,t[4]=s-p,t[5]=1-M-l,t[6]=b+v,t[7]=0,t[8]=c+m,t[9]=b-v,t[10]=1-M-f,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,t},n.frustum=function(t,a,n,r,o,e,u){var h=1/(n-a),i=1/(o-r),M=1/(e-u);return t[0]=2*e*h,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=2*e*i,t[6]=0,t[7]=0,t[8]=(n+a)*h,t[9]=(o+r)*i,t[10]=(u+e)*M,t[11]=-1,t[12]=0,t[13]=0,t[14]=u*e*2*M,t[15]=0,t},n.perspective=function(t,a,n,r,o){var e,u=1/Math.tan(a/2);t[0]=u/n,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=u,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[11]=-1,t[12]=0,t[13]=0,t[15]=0,null!=o&&o!==1/0?(e=1/(r-o),t[10]=(o+r)*e,t[14]=2*o*r*e):(t[10]=-1,t[14]=-2*r);return t},n.perspectiveFromFieldOfView=function(t,a,n,r){var o=Math.tan(a.upDegrees*Math.PI/180),e=Math.tan(a.downDegrees*Math.PI/180),u=Math.tan(a.leftDegrees*Math.PI/180),h=Math.tan(a.rightDegrees*Math.PI/180),i=2/(u+h),M=2/(o+e);return 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sigma\n", + "\n", + " ###### Bokeh Figures #######\n", + "\n", + "def peak_fig(signal, hist, edges, peak_idx, left, right):\n", + " \"\"\"General histogram plotter with peak location and left/right limits plotted\"\"\"\n", + " low = round(edges[left], 2)\n", + " hi = round(edges[right], 2)\n", + " fig = figure(\n", + " title='Used Intensity Distribution for {0}. Low/Hi: {1}/{2}'.format(signal, low, hi),\n", + " x_axis_label='Intensity Values',\n", + " y_axis_label='Counts'\n", + " )\n", + " fig.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:])\n", + " left_line = Span(location=edges[left], dimension='height', line_color='black')\n", + " right_line = Span(location=edges[right], dimension='height', line_color='black')\n", + " peak_line = Span(location=edges[peak_idx], dimension='height', line_color='red')\n", + " fig.renderers.extend([left_line, right_line, peak_line])\n", + "\n", + " return fig\n", + "\n", + "def azav_fig(ave_azav, peak, intensity, delta_bin):\n", + " \"\"\"Generate the azav fig for html file\"\"\"\n", + " x_vals = np.arange(len(ave_azav))\n", + " fig = figure(\n", + " title='Average Azimuthal Binned Array: Center - {0}, min/max - {1}/{2}, intensity - {3}'.format(peak, peak-delta_bin, peak+delta_bin, round(intensity, 2)),\n", + " x_axis_label='Bins',\n", + " y_axis_label='Intensity',\n", + " )\n", + "\n", + " peak_line = Span(location=peak, dimension='height', line_color='green', line_width=2)\n", + " lower_line = Span(location=peak-delta_bin, dimension='height', line_color='black')\n", + " upper_line = Span(location=peak+delta_bin, dimension='height', line_color='black')\n", + " ave_azav_curve = fig.scatter(x_vals, ave_azav)\n", + " fig.renderers.extend([peak_line, lower_line, upper_line])\n", + "\n", + " azav_legend = Legend(items=[\n", + " LegendItem(label='Azimuthal Average', renderers=[ave_azav_curve])\n", + " ])\n", + " fig.add_layout(azav_legend)\n", + "\n", + " return fig\n", + "\n", + "def intensity_hist(intensity_hist, edges):\n", + " fig = figure(\n", + " title='Intensity Histogram'\n", + " )\n", + " fig.quad(top=intensity_hist, bottom=0, left=edges[:-1], right=edges[1:])\n", + "\n", + " return fig\n", + "\n", + "def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma):\n", + " \"\"\"Simple plot of intensity vs peak value\"\"\"\n", + " fig = figure(\n", + " title='Peak value vs Intensity. Slope = {0}, Intercept = {1}'.format(round(slope, 2), round(intercept, 2)),\n", + " x_axis_label='Intensity Monitor Value',\n", + " y_axis_label='Peak Values'\n", + " )\n", + " fig.x_range.range_padding = fig.y_range.range_padding = 0\n", + " h, y_edge, x_edge = np.histogram2d(peak_vals, intensity, bins=100)\n", + " fig.image(image=[h], x=x_edge[0], y=y_edge[0], dh=y_edge[-1]-y_edge[0], dw=x_edge[-1]-x_edge[0], palette=\"Spectral11\")\n", + " color_mapper = LinearColorMapper(palette=\"Spectral11\", low=h.min(), high=h.max())\n", + " color_bar = ColorBar(color_mapper=color_mapper, location=(0,0))\n", + " fig.xaxis.bounds = [i0_low, i0_high]\n", + " fig.add_layout(color_bar, 'right')\n", + " fig.line(x, y, color='red')\n", + " fig.line(x, y - 1 * sigma, color='orange')\n", + " fig.line(x, y + 1 * sigma, color='orange')\n", + " return fig" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "# Find I0 distribution and filter out unused values\n", + "i0_data = np.array(i0_data)\n", + "i0_hist, i0_edges, i0_peak_idx, i0_left_idx, i0_right_idx = peak_lr(i0_data)\n", + "i0_low = i0_edges[i0_left_idx]\n", + "i0_high = i0_edges[i0_right_idx]\n", + "i0_idxs = np.where((i0_data > i0_low) & (i0_data < i0_high))\n", + "i0_data_use = i0_data[i0_idxs]\n", + "\n", + "# Filter on I0 data to get points we will evaluate\n", + "hist_peak, edges_peak, peak_idx, left_peak, right_peak = peak_lr(i0_data_use)\n", + "p = peak_fig('gdet', hist_peak, edges_peak, peak_idx, left_peak, right_peak)\n", + "\n", + "# Get the azav value we'll use\n", + "azav_use = [azav_data[idx] for idx in i0_idxs[0]]\n", + "ave_azav = np.array((np.sum(azav_use, axis=0)) / len(azav_use))\n", + "# Find the peak bin from average azav values\n", + "peak = calc_azav_peak(ave_azav)\n", + "peak=25\n", + "\n", + "# Get the integrated intensity and generate fig\n", + "integrated_intensity = get_integrated_intensity(ave_azav, peak, DELTA_BIN)\n", + "p1 = azav_fig(ave_azav, peak, integrated_intensity, DELTA_BIN)\n", + "\n", + "\n", + "# Go back through indices and find peak values for all the intensities\n", + "low = peak - DELTA_BIN\n", + "high = peak + DELTA_BIN\n", + "peak_vals = [azav[low:high].sum(axis=0) for azav in azav_use]\n", + "# Now fit I0 vs diffraction intensities\n", + "x, y, slope, intercept, sigma = fit_limits(i0_data_use, peak_vals, i0_low, i0_high)\n", + "p2 = intensity_vs_peak_fig(i0_data_use, peak_vals, x, y, slope, intercept, sigma)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 46, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
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+ "show(p)\n", + "show(p1)\n", + "show(p2)" + ] + }, + { + "cell_type": "code", + "execution_count": 56, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{'low_intercept': -3630.119742500365, 'ave_peak_intensity': 6332.59, 'delta_bin': 5, 'high_i0': 0.8466769609192851, 'ave_i0': 0.6414089038877722, 'peak_bin': 25, 'low_slope': 15036.018845158875, 'low_i0': 0.41789974458224605}\n" + ] + } + ], + "source": [ + "results = {\n", + " 'low_slope': slope,\n", + " 'low_intercept': intercept,\n", + " 'low_i0': i0_low,\n", + " 'high_i0': i0_high,\n", + " 'ave_i0': i0_data.mean(),\n", + " 'ave_peak_intensity': integrated_intensity,\n", + " 'peak_bin': peak,\n", + " 'delta_bin': DELTA_BIN\n", + "}\n", + "\n", + "\n", + "#After processing\n", + "# Peak bin\n", + "# low and hi delta_r around peak bin\n", + "# Io low bound and high bound\n", + "# Average Io\n", + "# Average integrated intensity\n", + "# slope and intercept of fit of 2D plot\n", + "# sigma around line fit\n", + "# Run number\n", + "\n", + "print(results)" + ] + }, + { + "cell_type": "code", + "execution_count": 54, + "metadata": {}, + "outputs": [ + { + "ename": "OSError", + "evalue": "[Errno 13] Permission denied: '/cds/home/opr/cxiopr/experiments/cxilv9518/jt_cal'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m\u001b[0m", + "\u001b[0;31mOSError\u001b[0mTraceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0mpath\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'/cds/home/opr/cxiopr/experiments/cxilv9518/jt_cal/run148/'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 6\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0misdir\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 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max_height=1000)\n", + "gspec[0:3, 0:3] = p\n", + "gspec[4:6, 0:3] = p1\n", + "gspec[7:9, 0:3] = p2\n", + "path = '/cds/home/opr/cxiopr/experiments/cxilv9518/jt_cal/run148/'\n", + "if not os.path.isdir(path):\n", + " os.makedirs(path)\n", + "gspec.save(''.join([path, 'report.html']))" + ] + }, + { + "cell_type": "code", + "execution_count": 51, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "LCLS-I py2", + "language": "python", + "name": "ana1-current" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.15" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/jet_tracking/jet_tracking_cal/jt_cal.py b/jet_tracking/jet_tracking_cal/jt_cal.py new file mode 100644 index 0000000..a6f6695 --- /dev/null +++ b/jet_tracking/jet_tracking_cal/jt_cal.py @@ -0,0 +1,410 @@ +import h5py +import numpy as np +import matplotlib.pyplot as plt +import logging +import re +import time +import psana +import yaml +from scipy.optimize import curve_fit +from argparse import ArgumentParser +import json +import os +import sys +from bokeh.plotting import figure, show, output_file +from bokeh.models import Span, Legend, LegendItem, ColorBar, LinearColorMapper +from bokeh.io import output_notebook +import panel as pn +from scipy.stats import gaussian_kde + +logger = logging.getLogger(__name__) + +# Constants +# Location of my branch for testing +JT_LOC = '/cds/home/a/aegger/jet_tracking/jet_tracking/mpi_scripts/' +# Number of bins +BINS = 100 +# Number of events to process +EVENTS = 1000 +# Percent of max in histogram to reject for I0 data +LR_THRESH = 0.1 +# Number of points at each end of azav to fit +LINE_FIT_POINTS = 5 +# Number of bins around peak to include in integrated intensity +DELTA_BIN = 5 + +# For now hold equations here since, will consolidate + +def get_r_masks(shape, bins=100): + """Function to generate radial masks for pixels to include in azav""" + center = (shape[1] / 2, shape[0] / 2) + x, y = np.meshgrid(np.arange(shape[1]) - center[0], \ + np.arange(shape[0]) - center[1]) + r = np.sqrt(x**2 + y**2) + max_r = np.max(r) + min_r = np.min(r) + bin_size = (max_r - min_r) / bins + radii = np.arange(1, max_r, bin_size) + masks = [] + for i in radii: + mask = (np.greater(r, i - bin_size) & np.less(r, i + bin_size)) + masks.append(mask) + + return masks + +def gaussian(x, a, mean, std, m, b): + """ + Equation for gaussian with linear component + + Parameters + ---------- + x : float + X-coordinate. + + a : float + Amplitude of Gaussian. + + mean : float + Mean of Gaussian. + + std : float + Standard deviation of Gaussian. + + m : float + Slope of linear baseline. + + b : float + Y-intercept of linear baseline. + + Returns + ------- + y : float + The y-coordinate for the given x-coordinate as defined by the + parameters given for the Gaussian on a slope with offset. + """ + return (a * np.exp(-((x - mean) / 2 / std) ** 2)) + (m * x + b) + +def fit_line(ave_azav, fit_points=LINE_FIT_POINTS): + """ + Fit the line from edges of array + + Parameters + ---------- + ave_azav: ndarray + The average azimuthal average from calibration data 1D array of floats. + + fit_points: int (Default: 5) + Number of points at each end of average azimuthal average to fit. + + Returns + ------- + m: float + slope of the fit + + b: float + y intercept of fit + """ + azav_len = len(ave_azav) + x0 = fit_points / 2 + x1 = azav_len - (fit_points / 2) + y0 = np.mean(ave_azav[:fit_points]) + y1 = np.mean(ave_azav[azav_len - fit_points:]) + m, b = np.polyfit((x0, x1), (y0, y1), 1) + + return m, b + +def peak_lr(array_data, threshold=LR_THRESH, bins=BINS): + """Find max of normal distribution from histogram, + search right and left until population falls below threshold, + will run into problems with bimodal distribution. This is naive, + look at KDE + + Parameters + ---------- + array_data: array like + 1D array data to cut on + + threshold: float + percent of max population to throw out. Upper/lower + + bins: int + Number of bins to generate for histogram we cut on + + Returns + ------- + hist: np.histogram + Histogram from array_data and bins + + edges: ndarray + array of floats for edges of histogram fit + + peak_idx: int + peak index of histogram + + i0_low: float + lower i0 value of cut on histogram + + i0_high: float + upper i0 value of cut on histogram + + i0_med: float + median i0 value + """ + hist, edges = np.histogram(array_data, bins=bins) + + # Find peak information + peak_val = hist.max() + peak_idx = np.where(hist == peak_val)[0][0] + i0_med = edges[peak_idx] + + #search right + right = np.argmax(hist[peak_idx:] < threshold * peak_val) + right += peak_idx + i0_high = edges[right] + + # search left + left_array = hist[:peak_idx] + left = peak_idx - np.argmax(left_array[::-1] < threshold * peak_val) + i0_low = edges[left] + + return hist, peak_idx, i0_low, i0_high, i0_med + +def calc_azav_peak(ave_azav): + """ + Get the peak from the gaussian fit with linear offset, if this + fails, just use the max value. This could also use KDE. + + Parameters + ---------- + ave_azav: ndarray + radially binned average azimuthal intensity from used curves + + Returns + ------- + peak: int + index of the bin with the peak intensity + """ + azav_len = len(ave_azav) + # Fit the gaussian with line offset, fails for skewed gaussian + m, b = fit_line(ave_azav) + x = np.arange(azav_len) + mean = np.sum(x * ave_azav) / np.sum(ave_azav) + std = np.sqrt(np.sum((x - mean) ** 2 / azav_len)) + + # Try to get the peak from fit + try: + # Guass/w line args + p0 = [max(ave_azav), mean, std, m, b] + popt, _ = curve_fit(gaussian, x, ave_azav, p0=p0) + peak = int(round(popt[1])) + except Exception as e: + logger.info('Failed to fit Gaussian, using peak') + peak = np.argmax(ave_azav) + + return peak + +def get_integrated_intensity(ave_azav, peak_bin, delta_bin=DELTA_BIN): + """ + Get the average integrated intensity. Sum the bin values from + the peak bin to delta bin on each side. + + Parameters + ---------- + ave_azav: ndarray + radially binned average azimuthal intensity from used curves + + peak_bin: int + peak radial bin + + delta_bin: int + number of bins on each side of peak to include in sum + + Returns + ------- + integrated_intensity: float + the calculated integrated intensity + """ + low = peak_bin - delta_bin + high = peak_bin + delta_bin + integrated_intensity = ave_azav[low: high].sum(axis=0) + + return integrated_intensity + +def fit_limits(i0_data, peak_vals, i_low, i_high, bins=100): + """ + Get the line fit and standard deviation of the plot of i0 + vs int_intensities. This will give information about + distribution of integrated intensities for given i0 values + + Parameters + ---------- + i0_data: ndarray + Values of incoming intensities used in calibration + + peak_vals: ndarray + Values of the integrated intensities corrspeconding to i0 values + + """ + m, b = np.polyfit(i0_data, peak_vals, 1) + x = np.linspace(i_low, i_high, bins) + sigma = np.std(peak_vals) + y = x * m + b + + return x, y, m, b, sigma + + ###### Bokeh Figures ####### + +def peak_fig(signal, hist, edges, peak_idx, left, right): + """General histogram plotter with peak location and + left/right limits plotted""" + low = round(edges[left], 2) + hi = round(edges[right], 2) + fig = figure( + title='Used Intensity Distribution for {0}. \ + Low/Hi: {1}/{2}'.format(signal, low, hi), + x_axis_label='Intensity Values', + y_axis_label='Counts' + ) + fig.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:]) + left_line = Span(location=edges[left], dimension='height', \ + line_color='black') + right_line = Span(location=edges[right], dimension='height', \ + line_color='black') + peak_line = Span(location=edges[peak_idx], dimension='height', \ + line_color='red') + fig.renderers.extend([left_line, right_line, peak_line]) + + return fig + +def azav_fig(ave_azav, peak, intensity, delta_bin): + """Generate the azav fig for html file""" + x_vals = np.arange(len(ave_azav)) + fig = figure( + title='Average Azimuthal Binned Array: Center - {0}, min/max - {1}/{2}, intensity - {3}'.format(peak, peak-delta_bin, peak+delta_bin, round(intensity, 2)), + x_axis_label='Bins', + y_axis_label='Intensity', + ) + + peak_line = Span(location=peak, dimension='height', line_color='green', line_width=2) + lower_line = Span(location=peak-delta_bin, dimension='height', line_color='black') + upper_line = Span(location=peak+delta_bin, dimension='height', line_color='black') + ave_azav_curve = fig.scatter(x_vals, ave_azav) + fig.renderers.extend([peak_line, lower_line, upper_line]) + + azav_legend = Legend(items=[ + LegendItem(label='Azimuthal Average', renderers=[ave_azav_curve]) + ]) + fig.add_layout(azav_legend) + + return fig + +def intensity_hist(intensity_hist, edges): + fig = figure( + title='Intensity Histogram' + ) + fig.quad(top=intensity_hist, bottom=0, left=edges[:-1], right=edges[1:]) + + return fig + +def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): + """Simple plot of intensity vs peak value""" + fig = figure( + title='Peak value vs Intensity. Slope = {0}, Intercept = {1}'.format(round(slope, 2), round(intercept, 2)), + x_axis_label='Intensity Monitor Value', + y_axis_label='Peak Values' + ) + fig.x_range.range_padding = fig.y_range.range_padding = 0 + h, y_edge, x_edge = np.histogram2d(peak_vals, intensity, bins=100) + fig.image(image=[h], x=x_edge[0], y=y_edge[0], dh=y_edge[-1]-y_edge[0], dw=x_edge[-1]-x_edge[0], palette="Spectral11") + color_mapper = LinearColorMapper(palette="Spectral11", low=h.min(), high=h.max()) + color_bar = ColorBar(color_mapper=color_mapper, location=(0,0)) + fig.xaxis.bounds = [i0_low, i0_high] + fig.add_layout(color_bar, 'right') + fig.line(x, y, color='red') + fig.line(x, y - 1 * sigma, color='orange') + fig.line(x, y + 1 * sigma, color='orange') + return fig + # 2d histogram with limits plotted + # gspec[10:12, 0:3] = intensity_vs_peak_fig(i0_data_use, azav_intensity_vals, x, y, m, b, sigma) + + # results_dir = args.results_dir + # if not results_dir: + # results_dir = f'{results_path}/results.html' + + # if not os.path.exists(results_dir): + # logger.debug('results directory does not exist, creating') + # os.makedirs(results_dir) + + # logger.debug(f'Saving html file to {results_dir}') + # gspec.save(f'{results_path}/results.html') + + # results = { + # 'i0_low': i0_low, + # 'i0_high': i0_high, + # 'peak_azav_bin': peak_azav_bin, + # 'left_azav_bin': left_azav_bin, + # 'right_azav_bin': right_azav_bin, + # 'slope_fit': m, + # 'intercept': b, + # 'sigma': sigma + # } + # cal_dir = args.cal_dir + # if not cal_dir: + # cal_dir = f'{cal_path}/Run_{run}' + + # write_html(cal_dir, results, run) + +if __name__ == '__main__': + parser = ArgumentParser() + parser.add_argument('--exp', type=str, default=(os.environ['EXPERIMENT'])) + parser.add_argument('--run', type=str, default=(os.environ['RUN_NUM'])) + parser.add_argument('--cfg', type=str, \ + default=(''.join([JT_LOC, 'mpi_scripts/mpi_configs/default_config.yml']))) + args = parser.parse_args() + + with open(''.join(['mpi_configs/', args.cfg_file])) as f: + yml_dict = yaml.load(f, Loader=yaml.FullLoader) + api_port = yml_dict['api_msg']['port'] + det_map = yml_dict['det_map'] + ipm_name = yml_dict['ipm']['name'] + ipm_det = yml_dict['ipm']['det'] + hutch = yml_dict['hutch'] + + # Setup data source + exp_run = ''.join(['exp=', args.exp, ':run=', args.run]) + exp_dir = ''.join(['/reg/d/psdm/', hutch, '/', args.exp, '/xtc/']) + dsname = ''.join([exp_run, ':smd:', 'dir=', exp_dir]) + ds = psana.DataSource(dsname) + + # Get the detectors from the config + detector = psana.Detector(det_map['name']) + ipm = psana.Detector(ipm_name) + masks = get_r_masks((2203, 2299), BINS) + i0_data = [] + azav_data=[] + + # Find I0 distribution and filter out unused values + i0_data = np.array(i0_data) + i0_hist, i0_peak_idx, i0_low, i0_high, i0_med = peak_lr(i0_data) + i0_idxs = np.where((i0_data > i0_low) & (i0_data < i0_high)) + i0_data_use = i0_data[i0_idxs] + p = peak_fig('gdet', i0_hist, i0_peak_idx, i0_low, i0_high) + + # Get the azav value we'll use + azav_use = [azav_data[idx] for idx in i0_idxs[0]] + ave_azav = np.array((np.sum(azav_use, axis=0)) / len(azav_use)) + # Find the peak bin from average azav values + peak = calc_azav_peak(ave_azav) + + # Get the integrated intensity and generate fig + integrated_intensity = get_integrated_intensity(ave_azav, peak, DELTA_BIN) + p1 = azav_fig(ave_azav, peak, integrated_intensity, DELTA_BIN) + + + # Go back through indices and find peak values for all the intensities + low = peak - DELTA_BIN + high = peak + DELTA_BIN + peak_vals = [azav[low:high].sum(axis=0) for azav in azav_use] + # Now fit I0 vs diffraction intensities + x, y, slope, intercept, sigma = fit_limits(i0_data_use, peak_vals, i0_low, i0_high) + p2 = intensity_vs_peak_fig(i0_data_use, peak_vals, x, y, slope, intercept, sigma) \ No newline at end of file diff --git a/jet_tracking/jet_tracking_cal/jt_cal_arp.py b/jet_tracking/jet_tracking_cal/jt_cal_arp.py new file mode 100644 index 0000000..656589b --- /dev/null +++ b/jet_tracking/jet_tracking_cal/jt_cal_arp.py @@ -0,0 +1,17 @@ +# EXPRUN = 'exp=cxilv9518:run=148' +# INFO = re.split('=|:', EXPRUN) +# EXP = INFO[1] +# HUTCH = EXP[:3] +# # Number of bins +# BINS = 100 +# # Number of events to process +# EVENTS = 1000 +# EXPDIR = ''.join(['/reg/d/psdm/', HUTCH, '/', EXP, '/xtc/']) +# DSNAME = ''.join([EXPRUN, ':smd:', 'dir=', EXPDIR]) +import os +from argparse import ArgumentParser + +parser = ArgumentParser() +parser.add_argument('--exp', type=str, default=(os.environ['EXPERIMENT'])) +parser.add_argument('--run', type=str, default=(os.environ['RUN_NUM'])) +parser.add_argument('--cfg', type=str, default=('')) \ No newline at end of file diff --git a/jet_tracking/jet_tracking_cal/submit_jt_arp.sh b/jet_tracking/jet_tracking_cal/submit_jt_arp.sh new file mode 100644 index 0000000..206b931 --- /dev/null +++ b/jet_tracking/jet_tracking_cal/submit_jt_arp.sh @@ -0,0 +1,5 @@ +#!/bin/bash +# Script to get the data for a jet tracking calibration +source /reg/g/psdm/etc/psconda.sh +ABS_PATH=/cds/home/a/aegger/jet_tracking/jet_tracking/jet_tracking_cal +sbatch --nodes=2 --time=5 $ABS_PATH/jt_cal.py "$@" \ No newline at end of file From b05e02944f7566bc9a52c104443bb9aeb91dd28e Mon Sep 17 00:00:00 2001 From: Adam Date: Tue, 3 Nov 2020 12:27:39 -0800 Subject: [PATCH 02/23] starting to test --- jet_tracking/jet_tracking_cal/jt_cal.py | 36 ++++++++----------- jet_tracking/jet_tracking_cal/jt_cal_arp.py | 17 --------- .../jet_tracking_cal/submit_jt_arp.sh | 4 +-- 3 files changed, 17 insertions(+), 40 deletions(-) delete mode 100644 jet_tracking/jet_tracking_cal/jt_cal_arp.py mode change 100644 => 100755 jet_tracking/jet_tracking_cal/submit_jt_arp.sh diff --git a/jet_tracking/jet_tracking_cal/jt_cal.py b/jet_tracking/jet_tracking_cal/jt_cal.py index a6f6695..19dff6d 100644 --- a/jet_tracking/jet_tracking_cal/jt_cal.py +++ b/jet_tracking/jet_tracking_cal/jt_cal.py @@ -135,12 +135,6 @@ def peak_lr(array_data, threshold=LR_THRESH, bins=BINS): hist: np.histogram Histogram from array_data and bins - edges: ndarray - array of floats for edges of histogram fit - - peak_idx: int - peak index of histogram - i0_low: float lower i0 value of cut on histogram @@ -167,7 +161,7 @@ def peak_lr(array_data, threshold=LR_THRESH, bins=BINS): left = peak_idx - np.argmax(left_array[::-1] < threshold * peak_val) i0_low = edges[left] - return hist, peak_idx, i0_low, i0_high, i0_med + return hist, i0_low, i0_high, i0_med def calc_azav_peak(ave_azav): """ @@ -254,23 +248,21 @@ def fit_limits(i0_data, peak_vals, i_low, i_high, bins=100): ###### Bokeh Figures ####### -def peak_fig(signal, hist, edges, peak_idx, left, right): +def peak_fig(signal, hist, med, low, high): """General histogram plotter with peak location and left/right limits plotted""" - low = round(edges[left], 2) - hi = round(edges[right], 2) fig = figure( title='Used Intensity Distribution for {0}. \ - Low/Hi: {1}/{2}'.format(signal, low, hi), + Low/Hi: {1}/{2}'.format(signal, low, high), x_axis_label='Intensity Values', y_axis_label='Counts' ) fig.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:]) - left_line = Span(location=edges[left], dimension='height', \ + left_line = Span(location=low, dimension='height', \ line_color='black') - right_line = Span(location=edges[right], dimension='height', \ + right_line = Span(location=high, dimension='height', \ line_color='black') - peak_line = Span(location=edges[peak_idx], dimension='height', \ + peak_line = Span(location=med, dimension='height', \ line_color='red') fig.renderers.extend([left_line, right_line, peak_line]) @@ -356,13 +348,15 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): if __name__ == '__main__': parser = ArgumentParser() - parser.add_argument('--exp', type=str, default=(os.environ['EXPERIMENT'])) - parser.add_argument('--run', type=str, default=(os.environ['RUN_NUM'])) + parser.add_argument('--exp', type=str, default=(os.environ.get('EXPERIMENT', None))) + parser.add_argument('--run', type=str, default=(os.environ.get('RUN_NUM', None))) parser.add_argument('--cfg', type=str, \ default=(''.join([JT_LOC, 'mpi_scripts/mpi_configs/default_config.yml']))) args = parser.parse_args() - with open(''.join(['mpi_configs/', args.cfg_file])) as f: + # All useful information should come from the config file + # This will be source of truth for starting point for each hutch for now + with open(args.cfg) as f: yml_dict = yaml.load(f, Loader=yaml.FullLoader) api_port = yml_dict['api_msg']['port'] det_map = yml_dict['det_map'] @@ -385,10 +379,11 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): # Find I0 distribution and filter out unused values i0_data = np.array(i0_data) - i0_hist, i0_peak_idx, i0_low, i0_high, i0_med = peak_lr(i0_data) + i0_hist, i0_low, i0_high, i0_med = peak_lr(i0_data) i0_idxs = np.where((i0_data > i0_low) & (i0_data < i0_high)) i0_data_use = i0_data[i0_idxs] - p = peak_fig('gdet', i0_hist, i0_peak_idx, i0_low, i0_high) + # Generate figure for i0 params + p = peak_fig('i0 Values', i0_hist, i0_med, i0_low, i0_high) # Get the azav value we'll use azav_use = [azav_data[idx] for idx in i0_idxs[0]] @@ -400,11 +395,10 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): integrated_intensity = get_integrated_intensity(ave_azav, peak, DELTA_BIN) p1 = azav_fig(ave_azav, peak, integrated_intensity, DELTA_BIN) - # Go back through indices and find peak values for all the intensities low = peak - DELTA_BIN high = peak + DELTA_BIN peak_vals = [azav[low:high].sum(axis=0) for azav in azav_use] # Now fit I0 vs diffraction intensities x, y, slope, intercept, sigma = fit_limits(i0_data_use, peak_vals, i0_low, i0_high) - p2 = intensity_vs_peak_fig(i0_data_use, peak_vals, x, y, slope, intercept, sigma) \ No newline at end of file + p2 = intensity_vs_peak_fig(i0_data_use, peak_vals, x, y, slope, intercept, sigma) diff --git a/jet_tracking/jet_tracking_cal/jt_cal_arp.py b/jet_tracking/jet_tracking_cal/jt_cal_arp.py deleted file mode 100644 index 656589b..0000000 --- a/jet_tracking/jet_tracking_cal/jt_cal_arp.py +++ /dev/null @@ -1,17 +0,0 @@ -# EXPRUN = 'exp=cxilv9518:run=148' -# INFO = re.split('=|:', EXPRUN) -# EXP = INFO[1] -# HUTCH = EXP[:3] -# # Number of bins -# BINS = 100 -# # Number of events to process -# EVENTS = 1000 -# EXPDIR = ''.join(['/reg/d/psdm/', HUTCH, '/', EXP, '/xtc/']) -# DSNAME = ''.join([EXPRUN, ':smd:', 'dir=', EXPDIR]) -import os -from argparse import ArgumentParser - -parser = ArgumentParser() -parser.add_argument('--exp', type=str, default=(os.environ['EXPERIMENT'])) -parser.add_argument('--run', type=str, default=(os.environ['RUN_NUM'])) -parser.add_argument('--cfg', type=str, default=('')) \ No newline at end of file diff --git a/jet_tracking/jet_tracking_cal/submit_jt_arp.sh b/jet_tracking/jet_tracking_cal/submit_jt_arp.sh old mode 100644 new mode 100755 index 206b931..4e619d5 --- a/jet_tracking/jet_tracking_cal/submit_jt_arp.sh +++ b/jet_tracking/jet_tracking_cal/submit_jt_arp.sh @@ -1,5 +1,5 @@ #!/bin/bash -# Script to get the data for a jet tracking calibration + source /reg/g/psdm/etc/psconda.sh ABS_PATH=/cds/home/a/aegger/jet_tracking/jet_tracking/jet_tracking_cal -sbatch --nodes=2 --time=5 $ABS_PATH/jt_cal.py "$@" \ No newline at end of file +sbatch --nodes=2 --time=5 $ABS_PATH/jt_cal.py "$@" From 9481a858f39e456674dc4acd0875ea5f24617960 Mon Sep 17 00:00:00 2001 From: Adam Egger Date: Tue, 3 Nov 2020 12:28:16 -0800 Subject: [PATCH 03/23] the default config file --- .../mpi_configs/default_config.yml | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 jet_tracking/mpi_scripts/mpi_configs/default_config.yml diff --git a/jet_tracking/mpi_scripts/mpi_configs/default_config.yml b/jet_tracking/mpi_scripts/mpi_configs/default_config.yml new file mode 100644 index 0000000..96034b1 --- /dev/null +++ b/jet_tracking/mpi_scripts/mpi_configs/default_config.yml @@ -0,0 +1,23 @@ +api_msg: + port: 5000 + +det_map: + name: 'jungfrau4M' + shape: + - 2203 + - 2299 + dtype: float32 + bins: 100 + +pv_map: + 1: 'CXI:JTRK:REQ:DIFF_INTENSITY' + 2: 'CXI:JTRK:REQ:I0' + +ipm: + name: 'FEEGasDetEnergy' + det: 'f_12_ENRC' + +hutch: 'cxi' +#ipm: +# name: 'CXI-DG2-BMMON' +# det: None From 576db3872ef43b046cdac6c8b635f1d7042c0329 Mon Sep 17 00:00:00 2001 From: Adam Date: Tue, 3 Nov 2020 12:58:45 -0800 Subject: [PATCH 04/23] correct conda env, fix bugs with plots --- jet_tracking/jet_tracking_cal/jt_cal.py | 48 +++++++++++++++---- .../jet_tracking_cal/submit_jt_arp.sh | 2 +- 2 files changed, 39 insertions(+), 11 deletions(-) diff --git a/jet_tracking/jet_tracking_cal/jt_cal.py b/jet_tracking/jet_tracking_cal/jt_cal.py index 19dff6d..e894410 100644 --- a/jet_tracking/jet_tracking_cal/jt_cal.py +++ b/jet_tracking/jet_tracking_cal/jt_cal.py @@ -21,7 +21,7 @@ # Constants # Location of my branch for testing -JT_LOC = '/cds/home/a/aegger/jet_tracking/jet_tracking/mpi_scripts/' +JT_LOC = '/cds/home/a/aegger/jet_tracking/jet_tracking/' # Number of bins BINS = 100 # Number of events to process @@ -257,7 +257,7 @@ def peak_fig(signal, hist, med, low, high): x_axis_label='Intensity Values', y_axis_label='Counts' ) - fig.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:]) + fig.quad(top=hist, bottom=0, left=low, right=high) left_line = Span(location=low, dimension='height', \ line_color='black') right_line = Span(location=high, dimension='height', \ @@ -272,14 +272,19 @@ def azav_fig(ave_azav, peak, intensity, delta_bin): """Generate the azav fig for html file""" x_vals = np.arange(len(ave_azav)) fig = figure( - title='Average Azimuthal Binned Array: Center - {0}, min/max - {1}/{2}, intensity - {3}'.format(peak, peak-delta_bin, peak+delta_bin, round(intensity, 2)), + title='Average Azimuthal Binned Array: Center - {0}, \ + min/max - {1}/{2}, intensity - {3}'.format(peak, \ + peak-delta_bin, peak+delta_bin, round(intensity, 2)), x_axis_label='Bins', y_axis_label='Intensity', ) - peak_line = Span(location=peak, dimension='height', line_color='green', line_width=2) - lower_line = Span(location=peak-delta_bin, dimension='height', line_color='black') - upper_line = Span(location=peak+delta_bin, dimension='height', line_color='black') + peak_line = Span(location=peak, dimension='height', \ + line_color='green', line_width=2) + lower_line = Span(location=peak-delta_bin, dimension='height', \ + line_color='black') + upper_line = Span(location=peak+delta_bin, dimension='height', \ + line_color='black') ave_azav_curve = fig.scatter(x_vals, ave_azav) fig.renderers.extend([peak_line, lower_line, upper_line]) @@ -301,13 +306,15 @@ def intensity_hist(intensity_hist, edges): def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): """Simple plot of intensity vs peak value""" fig = figure( - title='Peak value vs Intensity. Slope = {0}, Intercept = {1}'.format(round(slope, 2), round(intercept, 2)), + title='Peak value vs Intensity. Slope = {0}, Intercept = {1}'.\ + format(round(slope, 2), round(intercept, 2)), x_axis_label='Intensity Monitor Value', y_axis_label='Peak Values' ) fig.x_range.range_padding = fig.y_range.range_padding = 0 h, y_edge, x_edge = np.histogram2d(peak_vals, intensity, bins=100) - fig.image(image=[h], x=x_edge[0], y=y_edge[0], dh=y_edge[-1]-y_edge[0], dw=x_edge[-1]-x_edge[0], palette="Spectral11") + fig.image(image=[h], x=x_edge[0], y=y_edge[0], dh=y_edge[-1]-y_edge[0], \ + dw=x_edge[-1]-x_edge[0], palette="Spectral11") color_mapper = LinearColorMapper(palette="Spectral11", low=h.min(), high=h.max()) color_bar = ColorBar(color_mapper=color_mapper, location=(0,0)) fig.xaxis.bounds = [i0_low, i0_high] @@ -348,8 +355,10 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): if __name__ == '__main__': parser = ArgumentParser() - parser.add_argument('--exp', type=str, default=(os.environ.get('EXPERIMENT', None))) - parser.add_argument('--run', type=str, default=(os.environ.get('RUN_NUM', None))) + parser.add_argument('--exp', type=str, \ + default=(os.environ.get('EXPERIMENT', None))) + parser.add_argument('--run', type=str, \ + default=(os.environ.get('RUN_NUM', None))) parser.add_argument('--cfg', type=str, \ default=(''.join([JT_LOC, 'mpi_scripts/mpi_configs/default_config.yml']))) args = parser.parse_args() @@ -376,6 +385,25 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): masks = get_r_masks((2203, 2299), BINS) i0_data = [] azav_data=[] + ped = detector.pedestals(1)[0] + logger.info('starting to evaluate 1000 events') + print('starting to evaluate 1000 events') + for evt_idx, evt in enumerate(ds.events()): + if evt_idx % 100 == 0: + logger.info('finished {} events'.format(evt_idx)) + print('finished {} events'.format(evt_idx)) + raw = detector.raw_data(evt) - ped + image = detector.image(evt, raw) + azav = np.array([np.mean(image[mask]) for mask in masks]) + azav_data.append(azav) + try: + i0_data.append(ipm.get(evt).f_12_ENRC()) + except: + logger.warning('missing i0 for event {}'.format(evt_idx)) + i0_data.append(0.0) + + if evt_idx == 100: + break # Find I0 distribution and filter out unused values i0_data = np.array(i0_data) diff --git a/jet_tracking/jet_tracking_cal/submit_jt_arp.sh b/jet_tracking/jet_tracking_cal/submit_jt_arp.sh index 4e619d5..d6efc45 100755 --- a/jet_tracking/jet_tracking_cal/submit_jt_arp.sh +++ b/jet_tracking/jet_tracking_cal/submit_jt_arp.sh @@ -1,5 +1,5 @@ #!/bin/bash -source /reg/g/psdm/etc/psconda.sh +source /reg/g/psdm/sw/conda1/manage/bin/psconda.sh ABS_PATH=/cds/home/a/aegger/jet_tracking/jet_tracking/jet_tracking_cal sbatch --nodes=2 --time=5 $ABS_PATH/jt_cal.py "$@" From c5a57f7ce4287e46656bac812d3f7ed3b945429e Mon Sep 17 00:00:00 2001 From: Adam Date: Tue, 3 Nov 2020 16:14:23 -0800 Subject: [PATCH 05/23] couple of more args --- jet_tracking/jet_tracking_cal/jt_cal.py | 85 +++++++++++++------------ 1 file changed, 45 insertions(+), 40 deletions(-) diff --git a/jet_tracking/jet_tracking_cal/jt_cal.py b/jet_tracking/jet_tracking_cal/jt_cal.py index e894410..60777bb 100644 --- a/jet_tracking/jet_tracking_cal/jt_cal.py +++ b/jet_tracking/jet_tracking_cal/jt_cal.py @@ -323,35 +323,6 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): fig.line(x, y - 1 * sigma, color='orange') fig.line(x, y + 1 * sigma, color='orange') return fig - # 2d histogram with limits plotted - # gspec[10:12, 0:3] = intensity_vs_peak_fig(i0_data_use, azav_intensity_vals, x, y, m, b, sigma) - - # results_dir = args.results_dir - # if not results_dir: - # results_dir = f'{results_path}/results.html' - - # if not os.path.exists(results_dir): - # logger.debug('results directory does not exist, creating') - # os.makedirs(results_dir) - - # logger.debug(f'Saving html file to {results_dir}') - # gspec.save(f'{results_path}/results.html') - - # results = { - # 'i0_low': i0_low, - # 'i0_high': i0_high, - # 'peak_azav_bin': peak_azav_bin, - # 'left_azav_bin': left_azav_bin, - # 'right_azav_bin': right_azav_bin, - # 'slope_fit': m, - # 'intercept': b, - # 'sigma': sigma - # } - # cal_dir = args.cal_dir - # if not cal_dir: - # cal_dir = f'{cal_path}/Run_{run}' - - # write_html(cal_dir, results, run) if __name__ == '__main__': parser = ArgumentParser() @@ -361,28 +332,34 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): default=(os.environ.get('RUN_NUM', None))) parser.add_argument('--cfg', type=str, \ default=(''.join([JT_LOC, 'mpi_scripts/mpi_configs/default_config.yml']))) + parser.add_argument('--delta_bin', type=int, \ + default=(DELTA_BIN)) + parser.add_argument('--bins', type=int, \ + default=(BINS)) args = parser.parse_args() # All useful information should come from the config file # This will be source of truth for starting point for each hutch for now with open(args.cfg) as f: yml_dict = yaml.load(f, Loader=yaml.FullLoader) - api_port = yml_dict['api_msg']['port'] det_map = yml_dict['det_map'] ipm_name = yml_dict['ipm']['name'] ipm_det = yml_dict['ipm']['det'] hutch = yml_dict['hutch'] - # Setup data source + # Setup data source and write directories exp_run = ''.join(['exp=', args.exp, ':run=', args.run]) - exp_dir = ''.join(['/reg/d/psdm/', hutch, '/', args.exp, '/xtc/']) + base_dir = ''.join(['/cds/data/psdm/', hutch, '/', args.exp, '/']) + exp_dir = ''.join([base_dir, 'xtc/']) + plots_dir = ''.join([base_dir, 'stats/summary/']) + results_dir = ''.join([base_dir, 'results']) dsname = ''.join([exp_run, ':smd:', 'dir=', exp_dir]) ds = psana.DataSource(dsname) # Get the detectors from the config detector = psana.Detector(det_map['name']) ipm = psana.Detector(ipm_name) - masks = get_r_masks((2203, 2299), BINS) + masks = get_r_masks(det_map['shape'], args.bins) i0_data = [] azav_data=[] ped = detector.pedestals(1)[0] @@ -402,7 +379,7 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): logger.warning('missing i0 for event {}'.format(evt_idx)) i0_data.append(0.0) - if evt_idx == 100: + if evt_idx == 1000: break # Find I0 distribution and filter out unused values @@ -417,16 +394,44 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): azav_use = [azav_data[idx] for idx in i0_idxs[0]] ave_azav = np.array((np.sum(azav_use, axis=0)) / len(azav_use)) # Find the peak bin from average azav values - peak = calc_azav_peak(ave_azav) + peak_bin = calc_azav_peak(ave_azav) # Get the integrated intensity and generate fig - integrated_intensity = get_integrated_intensity(ave_azav, peak, DELTA_BIN) - p1 = azav_fig(ave_azav, peak, integrated_intensity, DELTA_BIN) + integrated_intensity = get_integrated_intensity(ave_azav, peak_bin, args.delta_bin) + p1 = azav_fig(ave_azav, peak_bin, integrated_intensity, args.delta_bin) # Go back through indices and find peak values for all the intensities - low = peak - DELTA_BIN - high = peak + DELTA_BIN - peak_vals = [azav[low:high].sum(axis=0) for azav in azav_use] + low_bin = peak_bin - args.delta_bin + high_bin = peak_bin + args.delta_bin + peak_vals = [azav[low_bin:high_bin].sum(axis=0) for azav in azav_use] # Now fit I0 vs diffraction intensities x, y, slope, intercept, sigma = fit_limits(i0_data_use, peak_vals, i0_low, i0_high) p2 = intensity_vs_peak_fig(i0_data_use, peak_vals, x, y, slope, intercept, sigma) + + # Ratio information + ratios = peak_vals / i0_data_use + mean_ratio = np.mean(ratios) + med_ratio = np.median(ratios) + std_ratio = np.std(ratios) + + # Accumulate results + results = { + 'i0_low': i0_low, + 'i0_high': i0_high, + 'peak_bin': peak_bin, + 'delta_bin': args.delta_bin, + 'mean_ratio': mean_ratio, + 'med_ratio': med_ratio, + 'std_ratio': std_ratio + } + + # Write results to file + with open(''.join([results_dir, '/', args.run, '_results']), 'w') as f: + json.dumps(results, f, sort_keys=True, indent=4) + + # Accumulate plots and write + gspec = pn.GridSpec() + gspec[0:3, 0:3] = p + gspec[4:6, 0:3] = p1 + gspec[7:9, 0:3] = p2 + gspec.save(''.join([plots_dir, 'results_', args.run, '.html'])) From 68ca13869a517b6a9a965f98a480904707dd6642 Mon Sep 17 00:00:00 2001 From: Adam Date: Tue, 3 Nov 2020 17:07:54 -0800 Subject: [PATCH 06/23] this is working --- jet_tracking/jet_tracking_cal/jt_cal.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/jet_tracking/jet_tracking_cal/jt_cal.py b/jet_tracking/jet_tracking_cal/jt_cal.py index 60777bb..1e1d6ca 100644 --- a/jet_tracking/jet_tracking_cal/jt_cal.py +++ b/jet_tracking/jet_tracking_cal/jt_cal.py @@ -364,7 +364,7 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): azav_data=[] ped = detector.pedestals(1)[0] logger.info('starting to evaluate 1000 events') - print('starting to evaluate 1000 events') + for evt_idx, evt in enumerate(ds.events()): if evt_idx % 100 == 0: logger.info('finished {} events'.format(evt_idx)) @@ -425,6 +425,8 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): 'std_ratio': std_ratio } + print(' found results ', results) + # Write results to file with open(''.join([results_dir, '/', args.run, '_results']), 'w') as f: json.dumps(results, f, sort_keys=True, indent=4) @@ -435,3 +437,5 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): gspec[4:6, 0:3] = p1 gspec[7:9, 0:3] = p2 gspec.save(''.join([plots_dir, 'results_', args.run, '.html'])) + + print('finished with calibration') From 709fb2744a7fbf2db66328f55bf59444ccd31e48 Mon Sep 17 00:00:00 2001 From: Adam Date: Wed, 25 Nov 2020 00:26:40 -0800 Subject: [PATCH 07/23] put all mpi work into repo --- jet_tracking/mpi_scripts/__init__.py | 0 jet_tracking/mpi_scripts/mpi_api.py | 35 +++++ .../mpi_configs/default_config.yml | 4 +- .../mpi_configs/smalldata_plot.yml | 71 +++++++++ jet_tracking/mpi_scripts/mpi_driver.py | 59 +++++++ jet_tracking/mpi_scripts/mpi_master.py | 145 ++++++++++++++++++ jet_tracking/mpi_scripts/mpi_worker.py | 137 +++++++++++++++++ jet_tracking/mpi_scripts/runMpiScript | 81 ++++++++++ jet_tracking/mpi_scripts/utils.py | 25 +++ 9 files changed, 554 insertions(+), 3 deletions(-) create mode 100644 jet_tracking/mpi_scripts/__init__.py create mode 100644 jet_tracking/mpi_scripts/mpi_api.py create mode 100644 jet_tracking/mpi_scripts/mpi_configs/smalldata_plot.yml create mode 100644 jet_tracking/mpi_scripts/mpi_driver.py create mode 100644 jet_tracking/mpi_scripts/mpi_master.py create mode 100644 jet_tracking/mpi_scripts/mpi_worker.py create mode 100755 jet_tracking/mpi_scripts/runMpiScript create mode 100644 jet_tracking/mpi_scripts/utils.py diff --git a/jet_tracking/mpi_scripts/__init__.py b/jet_tracking/mpi_scripts/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/jet_tracking/mpi_scripts/mpi_api.py b/jet_tracking/mpi_scripts/mpi_api.py new file mode 100644 index 0000000..17ee959 --- /dev/null +++ b/jet_tracking/mpi_scripts/mpi_api.py @@ -0,0 +1,35 @@ +import yaml +import zmq +import numpy as np +import argparse +parser = argparse.ArgumentParser() +parser.add_argument('--cfg_file', help='if specified, has information about what metadata to use', type=str, default='default_config.yml') +args = parser.parse_args() + +with open(''.join(['mpi_configs/', args.cfg_file])) as f: + yml_dict = yaml.load(f, Loader=yaml.FullLoader) + api_port = yml_dict['api_msg']['port'] + +context = zmq.Context() +socket = context.socket(zmq.PAIR) +socket.connect(''.join(['tcp://localhost:', str(api_port)])) + +# Example for subscribing to np arrays zmq +#context_data = zmq.Context() +#socket_data = context_data.socket(zmq.SUB) +#socket_data.connect(''.join(['tcp://localhost:', '8123'])) +#socket_data.subscribe("") # All topics +#while True: +# md = socket_data.recv_json(flags=0) +# msg = socket.recv(flags=0, copy=False, track=False) +# buf = memoryview(msg) +# data = np.frombuffer(buf, dtype=md['dtype']) +# print('data ', data.reshape(md['shape'])) + +def abort(): + """Abort MPI run""" + socket.send('abort') + +def pause(): + """Pause MPI run""" + socket.send('pause') diff --git a/jet_tracking/mpi_scripts/mpi_configs/default_config.yml b/jet_tracking/mpi_scripts/mpi_configs/default_config.yml index 96034b1..d1ee959 100644 --- a/jet_tracking/mpi_scripts/mpi_configs/default_config.yml +++ b/jet_tracking/mpi_scripts/mpi_configs/default_config.yml @@ -7,7 +7,7 @@ det_map: - 2203 - 2299 dtype: float32 - bins: 100 + bins: 50 pv_map: 1: 'CXI:JTRK:REQ:DIFF_INTENSITY' @@ -16,8 +16,6 @@ pv_map: ipm: name: 'FEEGasDetEnergy' det: 'f_12_ENRC' - -hutch: 'cxi' #ipm: # name: 'CXI-DG2-BMMON' # det: None diff --git a/jet_tracking/mpi_scripts/mpi_configs/smalldata_plot.yml b/jet_tracking/mpi_scripts/mpi_configs/smalldata_plot.yml new file mode 100644 index 0000000..8bc2555 --- /dev/null +++ b/jet_tracking/mpi_scripts/mpi_configs/smalldata_plot.yml @@ -0,0 +1,71 @@ +master: + server: daq-cxi-mon05 + port: 5000 + +ipm_ttampl: + port: 5014 + var1: ipm2__sum + var2: tt__AMPL + number_of_events: 1200 + width: 900 + height: 600 + updateRate: 2 + xRange: + - auto + - 0.4 + yRange: + - auto + - 2000. + +ipm_ROI: + port: 5015 + var1: ipm2__sum + var2: jungfrau512k__ROI_1 + number_of_events: 1200 + width: 900 + height: 600 + updateRate: 2 + xRange: + - auto + - 0.4 + yRange: + - auto + - 2000. + +ROI_scan: + port: 5016 + i0var: ipm2__sum + sigvar: jungfrau512k__ROI_1 + binWidth: 100 + binEntries: 50 + FilterVar: + - lightStatus__xray + - ipm2__sum + FilterVarMin: + - 0.5 + - 50 + FilterVarMax: + - 1.5 + - 1000000. + width: 900 + height: 600 + updateRate: 2 + xRange: + - auto + - 0.4 + yRange: + - auto + - 2000. + +tt_fltpos_time: + port: 5015 + var1: ttall + var1_idx: 0 + number_of_events: 14400 + width: 900 + height: 300 + updateRate: 5 + yRange: + - auto + - 2000. + diff --git a/jet_tracking/mpi_scripts/mpi_driver.py b/jet_tracking/mpi_scripts/mpi_driver.py new file mode 100644 index 0000000..94b80a2 --- /dev/null +++ b/jet_tracking/mpi_scripts/mpi_driver.py @@ -0,0 +1,59 @@ +# Local imports +from mpi_worker import MpiWorker +from mpi_master import MpiMaster +from utils import get_r_masks, get_evr_w_codes +from mpi4py import MPI +import psana +import yaml +import re +import argparse + +comm = MPI.COMM_WORLD +size = comm.Get_size() +rank = comm.Get_rank() + +# All the args +parser = argparse.ArgumentParser() +parser.add_argument('--exprun', help='psana experiment/run string (e.g. exp=xppd7114:run=43)', type=str, default='') +#parser.add_argument('--dsname', help='data source name', type=str, default='') +parser.add_argument('--nevts', help='number of events', default=50, type=int) +parser.add_argument('--cfg_file', help='if specified, has information about what metadata to use', type=str, default='default_config.yml') +args = parser.parse_args() + +# Two options for now, offline data or shared memory +if args.exprun: + info = re.split('=|:', args.exprun) + exp = info[1] + hutch = exp[:3] + exp_dir = ''.join(['/reg/d/psdm/', hutch, '/', exp, '/xtc/']) + dsname = ''.join([args.exprun, ':smd:', 'dir=', exp_dir]) +else: + dsname = 'shmem=psana.0:stop=no' + psana.setOption('psana.calib-dir', '/reg/d/psdm/cxi/cxilv9518/calib/') + +# Parse config file to hand to workers +with open(''.join(['mpi_configs/', args.cfg_file])) as f: + yml_dict = yaml.load(f, Loader=yaml.FullLoader) + api_port = yml_dict['api_msg']['port'] + det_map = yml_dict['det_map'] + ipm_name = yml_dict['ipm']['name'] + ipm_det = yml_dict['ipm']['det'] + pv_map = yml_dict['pv_map'] +print('here is pv map!!! ', pv_map) +# No way to do this only once with MPI +ds = psana.DataSource(dsname) +# Main detector we're looking at +detector = psana.Detector(det_map['name']) +# Intensity monitor, could be wave8 or gdet with detector +ipm = (psana.Detector(ipm_name), ipm_det) +# Because we never know hich evr will have event codes +evr = get_evr_w_codes(psana.DetNames()) +# Get the R masks, would be great to do this only once +r_mask = get_r_masks(det_map['shape']) +print(psana.DetNames()) +if rank == 0: + master = MpiMaster(rank, api_port, det_map, pv_map) + master.start_run() +else: + worker = MpiWorker(ds, args.nevts, detector, ipm, evr, r_mask) + worker.start_run() diff --git a/jet_tracking/mpi_scripts/mpi_master.py b/jet_tracking/mpi_scripts/mpi_master.py new file mode 100644 index 0000000..86bf061 --- /dev/null +++ b/jet_tracking/mpi_scripts/mpi_master.py @@ -0,0 +1,145 @@ +from mpi4py import MPI +import sys +import logging +import numpy as np +import zmq +import time +from epics import caput +from threading import Thread +from enum import Enum +from collections import deque + +f = '%(asctime)s - %(levelname)s - %(filename)s:%(funcName)s - %(message)s' +logging.basicConfig(level=logging.DEBUG, format=f) +logger = logging.getLogger(__name__) + + +class MpiMaster(object): + def __init__(self, rank, api_port, det_map, pv_map, psana=False, data_port=8123): + self._rank = rank + self._det_map = det_map + self._pv_map = pv_map + self._psana = psana + self._comm = MPI.COMM_WORLD + self._workers = range(self._comm.Get_size())[1:] + self._running = False + self._abort = False + self._queue = deque() + self._data_socket = self.get_data_socket() + self._msg_thread = Thread(target=self.start_msg_thread, args=(api_port,)) + self._msg_thread.start() + + @property + def rank(self): + """Master rank (should be 0)""" + return self._rank + + @property + def comm(self): + """Master communicator""" + return self._comm + + @property + def workers(self): + """Workers currently sending""" + return self._workers + + @property + def det_map(self): + """Detector info""" + return self._det_map + + @property + def queue(self): + """Queue for processing data from workers""" + return self._queue + + @property + def running(self): + """Check if master is running""" + return self._running + + @property + def abort(self): + """See if abort has been called""" + return self._abort + + @abort.setter + def abort(self, val): + """Set the abort flag""" + if isinstance(val, bool): + self._abort = val + + def get_data_socket(self, data_port=8123): + """Setup the socket we'll use for client data messaging""" + if self._psana: + context = zmq.Context() + socket = context.socket(zmq.PUB) + socket.bind(''.join(['tcp://*:', str(data_port)])) + return socket + + return None + + def start_run(self): + """Main process loop, we can probably get more async + but for now it's a one to one recive/send + """ + while not self.abort: + start = time.time() + # TODO: Generalize data length + data = np.empty(2, dtype=np.dtype(self.det_map['dtype'])) + req = self.comm.Irecv(data, source=MPI.ANY_SOURCE) + self.send_from_queue() + req.Wait() + self.queue.append(data) + print(time.time() - start) + MPI.Finalize() + +# status = MPI.Status() +# ready = self.comm.Iprobe(source=MPI.ANY_SOURCE, tag=MPI.ANY_TAG, status=status) +# if ready: +# data = np.empty(2, dtype=np.dtype(self.det_map['dtype'])) +# self.comm.Recv(data, source=status.Get_source(), tag=MPI.ANY_TAG, status=status) + + def start_msg_thread(self, api_port): + """The thread runs a PAIR communication and acts as server side, + this allows for control of the parameters during data aquisition + from some client (probably an API for user). Might do subpub if + we want messages to be handled by workers as well, or master can + broadcast information + """ + context = zmq.Context() + socket = context.socket(zmq.PAIR) + # TODO: make IP available arg + socket.bind(''.join(['tcp://*:', str(api_port)])) + while True: + message = socket.recv() + if message == 'abort': + self.abort = True + socket.send('aborted') + else: + print('Received Message with no definition ', message) + + def send_from_queue(self): + if len(self.queue) > 0: + data = self.queue.popleft() + if self._psana: + # Could need this if sending large arrays, + # Could end up getting md info from config file + md = dict( + dtype = str(data.dtype), + shape = data.shape + ) + self._data_socket.send_json(md, 0|zmq.NOBLOCK) + self._data_socket.send(data, 0, copy=False, track=False) + else: + # consider caput_many with lots, ok for now + #print('caputing data ', data) + #for k, v in self._pv_map: + #caput(v, data[k]) + ratio = data[1] / data[0] + caput('CXI:JTRK:REQ:DIFF_INTENSITY', data[1]) + caput('CXI:JTRK:REQ:I0', data[0]) + caput('CXI:JTRK:REQ:RATIO', ratio) + else: + pass diff --git a/jet_tracking/mpi_scripts/mpi_worker.py b/jet_tracking/mpi_scripts/mpi_worker.py new file mode 100644 index 0000000..bbc5c50 --- /dev/null +++ b/jet_tracking/mpi_scripts/mpi_worker.py @@ -0,0 +1,137 @@ +import psana +from psmon.plots import Image +import matplotlib.pyplot as plt +from matplotlib.colors import Normalize +from psmon import publish +import numpy as np +import os +import logging +import requests +import socket +import argparse +import sys +import time +import inspect +from mpi4py import MPI + +from smalldata_tools.SmallDataUtils import detData + +f = '%(asctime)s - %(levelname)s - %(filename)s:%(funcName)s - %(message)s' +logging.basicConfig(level=logging.DEBUG, format=f) +logger = logging.getLogger(__name__) + + +class MpiWorker(object): + """This worker will collect events and do whatever + necessary processing, then send to master""" + def __init__(self, ds, evnt_lim, detector, ipm, evr, r_mask, latency=0.5, event_code=40, plot=False, peak_bin=25, delta_bin=5): + self._ds = ds # We probably need to use kwargs to make this general + self._evnt_lim = evnt_lim + self._detector = detector + self._ipm = ipm + self._evr = evr + self._comm = MPI.COMM_WORLD + self._rank = self._comm.Get_rank() + self._r_mask = r_mask + self._plot = plot + self._latency = latency + self._event_code = event_code + self._peak_bin = peak_bin + self._delta_bin = delta_bin + self._state = None + + @property + def rank(self): + """Worker ID""" + return self._rank + + @property + def evnt_lim(self): + """Number of events for worker to process""" + return self._evnt_lim + + @property + def ds(self): + """DataSource object""" + return self._ds + + @property + def detector(self): + """Detectors to get data from""" + return self._detector + + @property + def comm(self): + """MPI communicator""" + return self._comm + + @property + def ipm(self): + """IPM Detector""" + return self._ipm + + @property + def evr(self): + """EVR detector""" + return self._evr + + @property + def plot(self): + """Whether we should plot detector""" + return self._plot + + @property + def latency(self): + """Max latency allowed between event and results""" + return self._latency + + @property + def event_code(self): + """Event Code to trigger data collection on""" + return self._event_code + + @property + def peak_bin(self): + return self._peak_bin + + @peak_bin.setter + def peak_bin(self, peak_bin): + try: + self._peak_bin = int(peak_bin) + except: + logger.warning('You must provide int for peak bin') + + @property + def delta_bin(self): + return self._delta_bin + + @delta_bin.setter + def delta_bin(self, delta_bin): + try: + self._delta_bin = int(delta_bin) + except: + logger.warning('You must provide int for delta bin') + + def start_run(self): + """Worker should handle any calculations""" + #mask_det = det.mask(188, unbond=True, unbondnbrs=True, status=True, edges=True, central=True) + ped = self.detector.pedestals(1)[0] + for evt_idx, evt in enumerate(self.ds.events()): + if self.event_code not in self.evr.eventCodes(evt): + continue + low_bin = self.peak_bin - self.delta_bin + hi_bin = self.peak_bin + self.delta_bin + raw = (self.detector.raw_data(evt) - ped) + data = self.detector.image(evt, raw) + az_bins = np.array([np.mean(data[mask]) for mask in self._r_mask[low_bin:hi_bin]]) + intensity = np.sum(az_bins) + try: + i0 = self.ipm[0].get(evt) + if self.ipm[1]: + det = getattr(i0, self.ipm[1]) + i0 = det() + except: + i0 = 0.0 + + packet = np.array([i0, intensity], dtype='float32') + self.comm.Isend(packet, dest=0, tag=self.rank) diff --git a/jet_tracking/mpi_scripts/runMpiScript b/jet_tracking/mpi_scripts/runMpiScript new file mode 100755 index 0000000..fa00b70 --- /dev/null +++ b/jet_tracking/mpi_scripts/runMpiScript @@ -0,0 +1,81 @@ +#!/bin/bash + +usage() +{ +cat << EOF +$(basename "$0"): + Script to launch an mpirun + + OPTIONS: + -h|--help + Definition of options + -e|--exprun + Experiment and run name in format exp=xppd7114:run=43 + -d|--dsname + Data source name to gather events from + -n|--nevts + Number of events for each worker to process + -c|--cfgfile + Config file to load with damage/vars, and other things to parse for data aquisition + -p|--processors + Number of cores to use (available workers -1 for master) +EOF +} + +for arg in "$@" +do + case $arg in + -h|--help) + usage exit + ;; + -e|--exprun) + EXPRUN="$2" + shift + shift + ;; + -d|--dsname) + DSNAME="$2" + shift + shift + ;; + -n|--nevts) + NEVTS="$2" + shift + shift + ;; + -c|--cfgfile) + CFGFILE="$2" + shift + shift + ;; + -p|--processors) + PROC="$2" + shift + shift + ;; + esac +done + +# Pull out mpi_driver.py args +ARGS='' +if [[ -v EXPRUN ]]; then + ARGS+=' --exprun '$EXPRUN +fi +if [[ -v DSNAME ]]; then + ARGS+=' --dsname '$DSNAME +fi +if [[ -v NEVTS ]]; then + ARGS+=' --nevts '$NEVTS +fi +if [[ -v CFGFILE ]]; then + ARGS+=' --cfg_file '$CFGFILE +fi + +# If user doesn't specify use minimum required +PROC=${PROC:='2'} + +source /reg/g/pcds/setup/pathmunge.sh +source /reg/g/psdm/sw/conda1/manage/bin/psconda.sh +cd /reg/neh/home/aegger/smalldata_tools/mpi_scripts +pythonpathmunge '/reg/neh/home/aegger/smalldata_tools' +`which mpirun` -n $PROC python mpi_driver.py $ARGS diff --git a/jet_tracking/mpi_scripts/utils.py b/jet_tracking/mpi_scripts/utils.py new file mode 100644 index 0000000..e859690 --- /dev/null +++ b/jet_tracking/mpi_scripts/utils.py @@ -0,0 +1,25 @@ +import numpy as np +import psana + +def get_r_masks(shape, bins=50): + """Function to generate radial masks for pixels to include in azav""" + center = (shape[1] / 2, shape[0] / 2) + x, y = np.meshgrid(np.arange(shape[1]) - center[0], np.arange(shape[0]) - center[1]) + R = np.sqrt(x**2 + y**2) + max_R = np.max(R) + min_R = np.min(R) + bin_size = (max_R - min_R) / bins + radii = np.arange(1, max_R, bin_size) + masks = [] + for i in radii: + mask = (np.greater(R, i - bin_size) & np.less(R, i + bin_size)) + masks.append(mask) + + return masks + +def get_evr_w_codes(det_names): + """Get the evr with the event codes, yes this changes...""" + evr_keys = [det[1] for det in det_names if 'evr' in det[1]] + evr_dict = {k: psana.Detector(k)._fetch_configs()[0].neventcodes() + for k in evr_keys} + return psana.Detector(max(evr_dict, key=evr_dict.get)) From 375e1eb694f92bc369443b520d00ca5f00e9d0b5 Mon Sep 17 00:00:00 2001 From: Adam Date: Wed, 10 Mar 2021 15:28:49 -0800 Subject: [PATCH 08/23] MNT: Remove notebook --- .../jet_tracking_cal/jet_tracking_cal.ipynb | 25803 ---------------- 1 file changed, 25803 deletions(-) delete mode 100644 jet_tracking/jet_tracking_cal/jet_tracking_cal.ipynb diff --git a/jet_tracking/jet_tracking_cal/jet_tracking_cal.ipynb b/jet_tracking/jet_tracking_cal/jet_tracking_cal.ipynb deleted file mode 100644 index 3851b40..0000000 --- a/jet_tracking/jet_tracking_cal/jet_tracking_cal.ipynb +++ /dev/null @@ -1,25803 +0,0 @@ -{ - 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\n", - " \n", - " Loading BokehJS ...\n", - "
" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "application/javascript": [ - "\n", - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " var force = true;\n", - "\n", - " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", - " root._bokeh_onload_callbacks = [];\n", - " root._bokeh_is_loading = undefined;\n", - " }\n", - "\n", - " var JS_MIME_TYPE = 'application/javascript';\n", - " var HTML_MIME_TYPE = 'text/html';\n", - " var EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", - " var CLASS_NAME = 'output_bokeh rendered_html';\n", - "\n", - " /**\n", - " * Render data to the DOM node\n", - " */\n", - " function render(props, node) {\n", - " var script = document.createElement(\"script\");\n", - " node.appendChild(script);\n", - " }\n", - "\n", - " /**\n", - " * Handle when an output is cleared or removed\n", - " */\n", - " function handleClearOutput(event, handle) {\n", - " var cell = handle.cell;\n", - "\n", - " var id = cell.output_area._bokeh_element_id;\n", - " var server_id = cell.output_area._bokeh_server_id;\n", - " // Clean up Bokeh references\n", - " if (id != null && id in Bokeh.index) {\n", - " Bokeh.index[id].model.document.clear();\n", - " delete Bokeh.index[id];\n", - " }\n", - "\n", - " if (server_id !== undefined) {\n", - " // Clean up Bokeh references\n", - " var cmd = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", - " cell.notebook.kernel.execute(cmd, {\n", - " iopub: {\n", - " output: function(msg) {\n", - " var id = msg.content.text.trim();\n", - " if (id in Bokeh.index) {\n", - " Bokeh.index[id].model.document.clear();\n", - " delete Bokeh.index[id];\n", - " }\n", - " }\n", - " }\n", - " });\n", - " // Destroy server and session\n", - " var cmd = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", - " cell.notebook.kernel.execute(cmd);\n", - " }\n", - " }\n", - "\n", - " /**\n", - " * Handle when a new output is added\n", - " */\n", - " function handleAddOutput(event, handle) {\n", - " var output_area = handle.output_area;\n", - " var output = handle.output;\n", - "\n", - " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", - " if ((output.output_type != \"display_data\") || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n", - " return\n", - " }\n", - "\n", - " var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", - "\n", - " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", - " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", - " // store reference to embed id on output_area\n", - " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", - " }\n", - " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", - " var bk_div = document.createElement(\"div\");\n", - " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", - " var script_attrs = bk_div.children[0].attributes;\n", - " for (var i = 0; i < script_attrs.length; i++) {\n", - " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", - " }\n", - " // store reference to server id on output_area\n", - " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", - " }\n", - " }\n", - "\n", - " function register_renderer(events, OutputArea) {\n", - "\n", - " function append_mime(data, metadata, element) {\n", - " // create a DOM node to render to\n", - " var toinsert = this.create_output_subarea(\n", - " metadata,\n", - " CLASS_NAME,\n", - " EXEC_MIME_TYPE\n", - " );\n", - " this.keyboard_manager.register_events(toinsert);\n", - " // Render to node\n", - " var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", - " render(props, toinsert[toinsert.length - 1]);\n", - " element.append(toinsert);\n", - " return toinsert\n", - " }\n", - "\n", - " /* Handle when an output is cleared or removed */\n", - " events.on('clear_output.CodeCell', handleClearOutput);\n", - " events.on('delete.Cell', handleClearOutput);\n", - "\n", - " /* Handle when a new output is added */\n", - " events.on('output_added.OutputArea', handleAddOutput);\n", - "\n", - " /**\n", - " * Register the mime type and append_mime function with output_area\n", - " */\n", - " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", - " /* Is output safe? */\n", - " safe: true,\n", - " /* Index of renderer in `output_area.display_order` */\n", - " index: 0\n", - " });\n", - " }\n", - "\n", - " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", - " if (root.Jupyter !== undefined) {\n", - " var events = require('base/js/events');\n", - " var OutputArea = require('notebook/js/outputarea').OutputArea;\n", - "\n", - " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", - " register_renderer(events, OutputArea);\n", - " }\n", - " }\n", - "\n", - " \n", - " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", - " root._bokeh_timeout = Date.now() + 5000;\n", - " root._bokeh_failed_load = false;\n", - " }\n", - "\n", - " var NB_LOAD_WARNING = {'data': {'text/html':\n", - " \"
\\n\"+\n", - " \"

\\n\"+\n", - " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", - " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", - " \"

\\n\"+\n", - " \"
    \\n\"+\n", - " \"
  • re-rerun `output_notebook()` to attempt to load from CDN again, or
    • \\n\"+\n", - " \"
  • use INLINE resources instead, as so:
    • \\n\"+\n", - " \"
\\n\"+\n", - " \"\\n\"+\n", - " \"from bokeh.resources import INLINE\\n\"+\n", - " \"output_notebook(resources=INLINE)\\n\"+\n", - " \"\\n\"+\n", - " \"
\"}};\n", - "\n", - " function display_loaded() {\n", - " var el = document.getElementById(\"1001\");\n", - " if (el != null) {\n", - " el.textContent = \"BokehJS is loading...\";\n", - " }\n", - " if (root.Bokeh !== undefined) {\n", - " if (el != null) {\n", - " el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n", - " }\n", - " } else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(display_loaded, 100)\n", - " }\n", - " }\n", - "\n", - "\n", - " function run_callbacks() {\n", - " try {\n", - " root._bokeh_onload_callbacks.forEach(function(callback) {\n", - " if (callback != null)\n", - " callback();\n", - " });\n", - " } finally {\n", - " delete root._bokeh_onload_callbacks\n", - " }\n", - " console.debug(\"Bokeh: all callbacks have finished\");\n", - " }\n", - "\n", - " function load_libs(css_urls, js_urls, callback) {\n", - " if (css_urls == null) css_urls = [];\n", - " if (js_urls == null) js_urls = [];\n", - "\n", - " root._bokeh_onload_callbacks.push(callback);\n", - " if (root._bokeh_is_loading > 0) {\n", - " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", - " return null;\n", - " }\n", - " if (js_urls == null || js_urls.length === 0) {\n", - " run_callbacks();\n", - " return null;\n", - " }\n", - " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", - " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", - "\n", - " function on_load() {\n", - " root._bokeh_is_loading--;\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", - " run_callbacks()\n", - " }\n", - " }\n", - "\n", - " function on_error() {\n", - " console.error(\"failed to load \" + url);\n", - " }\n", - "\n", - " for (var i = 0; i < css_urls.length; i++) {\n", - " var url = css_urls[i];\n", - " const element = document.createElement(\"link\");\n", - " element.onload = on_load;\n", - " element.onerror = on_error;\n", - " element.rel = \"stylesheet\";\n", - " element.type = \"text/css\";\n", - " element.href = url;\n", - " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " for (var i = 0; i < js_urls.length; i++) {\n", - " var url = js_urls[i];\n", - " var element = document.createElement('script');\n", - " element.onload = on_load;\n", - " element.onerror = on_error;\n", - " element.async = false;\n", - " element.src = url;\n", - " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " document.head.appendChild(element);\n", - " }\n", - " };var element = document.getElementById(\"1001\");\n", - " if (element == null) {\n", - " console.error(\"Bokeh: ERROR: autoload.js configured with elementid '1001' but no matching script tag was found. \")\n", - " return false;\n", - " }\n", - "\n", - " function inject_raw_css(css) {\n", - " const element = document.createElement(\"style\");\n", - " element.appendChild(document.createTextNode(css));\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " \n", - " var js_urls = [\"https://cdn.pydata.org/bokeh/release/bokeh-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-tables-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-gl-1.4.0.min.js\"];\n", - " var css_urls = [];\n", - " \n", - "\n", - " var inline_js = [\n", - " function(Bokeh) {\n", - " inject_raw_css(\".widget-box {\\n\\tmin-height: 20px;\\n\\tbackground-color: #f5f5f5;\\n\\tborder: 1px solid #e3e3e3 !important;\\n\\tborder-radius: 4px;\\n\\t-webkit-box-shadow: inset 0 1px 1px rgba(0,0,0,.05);\\n\\tbox-shadow: inset 0 1px 1px rgba(0,0,0,.05);\\n\\toverflow-x: hidden;\\n\\toverflow-y: hidden;\\n}\\n\\n.scrollable {\\n overflow: scroll;\\n}\\n\\nprogress {\\n\\tappearance: none;\\n\\t-moz-appearance: none;\\n\\t-webkit-appearance: none;\\n\\n\\tborder: none;\\n\\theight: 20px;\\n\\tbackground-color: whiteSmoke;\\n\\tborder-radius: 3px;\\n\\tbox-shadow: 0 2px 3px rgba(0,0,0,.5) inset;\\n\\tcolor: royalblue;\\n\\tposition: relative;\\n\\tmargin: 0 0 1.5em;\\n}\\n\\nprogress[value]::-webkit-progress-bar {\\n\\tbackground-color: whiteSmoke;\\n\\tborder-radius: 3px;\\n\\tbox-shadow: 0 2px 3px rgba(0,0,0,.5) inset;\\n}\\n\\nprogress[value]::-webkit-progress-value {\\n\\tposition: relative;\\n\\n\\tbackground-size: 35px 20px, 100% 100%, 100% 100%;\\n\\tborder-radius:3px;\\n}\\n\\nprogress.active:not([value])::before {\\n\\tbackground-position: 10%;\\n\\tanimation-name: stripes;\\n\\tanimation-duration: 3s;\\n\\tanimation-timing-function: linear;\\n\\tanimation-iteration-count: infinite;\\n}\\n\\nprogress[value]::-moz-progress-bar {\\n\\tbackground-size: 35px 20px, 100% 100%, 100% 100%;\\n\\tborder-radius:3px;\\n}\\n\\nprogress:not([value])::-moz-progress-bar {\\n\\tborder-radius:3px;\\n\\tbackground:\\n\\tlinear-gradient(-45deg, transparent 33%, rgba(0, 0, 0, 0.2) 33%, rgba(0, 0, 0, 0.2) 66%, transparent 66%) left/2.5em 1.5em;\\n\\n}\\n\\nprogress.active:not([value])::-moz-progress-bar {\\n\\tbackground-position: 10%;\\n\\tanimation-name: stripes;\\n\\tanimation-duration: 3s;\\n\\tanimation-timing-function: linear;\\n\\tanimation-iteration-count: infinite;\\n}\\n\\nprogress.active:not([value])::-webkit-progress-bar {\\n\\tbackground-position: 10%;\\n\\tanimation-name: stripes;\\n\\tanimation-duration: 3s;\\n\\tanimation-timing-function: linear;\\n\\tanimation-iteration-count: infinite;\\n}\\n\\nprogress.primary[value]::-webkit-progress-value { background-color: #007bff; }\\nprogress.primary:not([value])::before { background-color: #007bff; }\\nprogress.primary:not([value])::-webkit-progress-bar { background-color: #007bff; }\\nprogress.primary::-moz-progress-bar { background-color: #007bff; }\\n\\nprogress.secondary[value]::-webkit-progress-value { background-color: #6c757d; }\\nprogress.secondary:not([value])::before { background-color: #6c757d; }\\nprogress.secondary:not([value])::-webkit-progress-bar { background-color: #6c757d; }\\nprogress.secondary::-moz-progress-bar { background-color: #6c757d; }\\n\\nprogress.success[value]::-webkit-progress-value { background-color: #28a745; }\\nprogress.success:not([value])::before { background-color: #28a745; }\\nprogress.success:not([value])::-webkit-progress-bar { background-color: #28a745; }\\nprogress.success::-moz-progress-bar { background-color: #28a745; }\\n\\nprogress.danger[value]::-webkit-progress-value { background-color: #dc3545; }\\nprogress.danger:not([value])::before { background-color: #dc3545; }\\nprogress.danger:not([value])::-webkit-progress-bar { background-color: #dc3545; }\\nprogress.danger::-moz-progress-bar { background-color: #dc3545; }\\n\\nprogress.warning[value]::-webkit-progress-value { background-color: #ffc107; }\\nprogress.warning:not([value])::before { background-color: #ffc107; }\\nprogress.warning:not([value])::-webkit-progress-bar { background-color: #ffc107; }\\nprogress.warning::-moz-progress-bar { background-color: #ffc107; }\\n\\nprogress.info[value]::-webkit-progress-value { background-color: #17a2b8; }\\nprogress.info:not([value])::before { background-color: #17a2b8; }\\nprogress.info:not([value])::-webkit-progress-bar { background-color: #17a2b8; }\\nprogress.info::-moz-progress-bar { background-color: #17a2b8; }\\n\\nprogress.light[value]::-webkit-progress-value { background-color: #f8f9fa; }\\nprogress.light:not([value])::before { background-color: #f8f9fa; }\\nprogress.light:not([value])::-webkit-progress-bar { background-color: #f8f9fa; }\\nprogress.light::-moz-progress-bar { background-color: #f8f9fa; }\\n\\nprogress.dark[value]::-webkit-progress-value { background-color: #343a40; }\\nprogress.dark:not([value])::-webkit-progress-bar { background-color: #343a40; }\\nprogress.dark:not([value])::before { background-color: #343a40; }\\nprogress.dark::-moz-progress-bar { background-color: #343a40; }\\n\\nprogress:not([value])::-webkit-progress-bar {\\n\\tborder-radius: 3px;\\n\\tbackground:\\n\\tlinear-gradient(-45deg, transparent 33%, rgba(0, 0, 0, 0.2) 33%, rgba(0, 0, 0, 0.2) 66%, transparent 66%) left/2.5em 1.5em;\\n}\\nprogress:not([value])::before {\\n\\tcontent:\\\" \\\";\\n\\tposition:absolute;\\n\\theight: 20px;\\n\\ttop:0;\\n\\tleft:0;\\n\\tright:0;\\n\\tbottom:0;\\n\\tborder-radius: 3px;\\n\\tbackground:\\n\\tlinear-gradient(-45deg, transparent 33%, rgba(0, 0, 0, 0.2) 33%, rgba(0, 0, 0, 0.2) 66%, transparent 66%) left/2.5em 1.5em;\\n}\\n\\n@keyframes stripes {\\n from {background-position: 0%}\\n to {background-position: 100%}\\n}\");\n", - " },\n", - " function(Bokeh) {\n", - " inject_raw_css(\".json-formatter-row {\\n font-family: monospace;\\n}\\n.json-formatter-row,\\n.json-formatter-row a,\\n.json-formatter-row a:hover {\\n color: black;\\n text-decoration: none;\\n}\\n.json-formatter-row .json-formatter-row {\\n margin-left: 1rem;\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty {\\n opacity: 0.5;\\n margin-left: 1rem;\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty:after {\\n display: none;\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-object:after {\\n content: \\\"No properties\\\";\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-array:after {\\n content: \\\"[]\\\";\\n}\\n.json-formatter-row .json-formatter-string,\\n.json-formatter-row .json-formatter-stringifiable {\\n color: green;\\n white-space: pre;\\n word-wrap: break-word;\\n}\\n.json-formatter-row .json-formatter-number {\\n color: blue;\\n}\\n.json-formatter-row .json-formatter-boolean {\\n color: red;\\n}\\n.json-formatter-row .json-formatter-null {\\n color: #855A00;\\n}\\n.json-formatter-row .json-formatter-undefined {\\n color: #ca0b69;\\n}\\n.json-formatter-row .json-formatter-function {\\n color: #FF20ED;\\n}\\n.json-formatter-row .json-formatter-date {\\n background-color: rgba(0, 0, 0, 0.05);\\n}\\n.json-formatter-row .json-formatter-url {\\n text-decoration: underline;\\n color: blue;\\n cursor: pointer;\\n}\\n.json-formatter-row .json-formatter-bracket {\\n color: blue;\\n}\\n.json-formatter-row .json-formatter-key {\\n color: #00008B;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-row .json-formatter-toggler-link {\\n cursor: pointer;\\n}\\n.json-formatter-row .json-formatter-toggler {\\n line-height: 1.2rem;\\n font-size: 0.7rem;\\n vertical-align: middle;\\n opacity: 0.6;\\n cursor: pointer;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-row .json-formatter-toggler:after {\\n display: inline-block;\\n transition: transform 100ms ease-in;\\n content: \\\"\\\\25BA\\\";\\n}\\n.json-formatter-row > a > .json-formatter-preview-text {\\n opacity: 0;\\n transition: opacity 0.15s ease-in;\\n font-style: italic;\\n}\\n.json-formatter-row:hover > a > .json-formatter-preview-text {\\n opacity: 0.6;\\n}\\n.json-formatter-row.json-formatter-open > .json-formatter-toggler-link .json-formatter-toggler:after {\\n transform: rotate(90deg);\\n}\\n.json-formatter-row.json-formatter-open > .json-formatter-children:after {\\n display: inline-block;\\n}\\n.json-formatter-row.json-formatter-open > a > .json-formatter-preview-text {\\n display: none;\\n}\\n.json-formatter-row.json-formatter-open.json-formatter-empty:after {\\n display: block;\\n}\\n.json-formatter-dark.json-formatter-row {\\n font-family: monospace;\\n}\\n.json-formatter-dark.json-formatter-row,\\n.json-formatter-dark.json-formatter-row a,\\n.json-formatter-dark.json-formatter-row a:hover {\\n color: white;\\n text-decoration: none;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-row {\\n margin-left: 1rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty {\\n opacity: 0.5;\\n margin-left: 1rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty:after {\\n display: none;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-object:after {\\n content: \\\"No properties\\\";\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-array:after {\\n content: \\\"[]\\\";\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-string,\\n.json-formatter-dark.json-formatter-row .json-formatter-stringifiable {\\n color: #31F031;\\n white-space: pre;\\n word-wrap: break-word;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-number {\\n color: #66C2FF;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-boolean {\\n color: #EC4242;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-null {\\n color: #EEC97D;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-undefined {\\n color: #ef8fbe;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-function {\\n color: #FD48CB;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-date {\\n background-color: rgba(255, 255, 255, 0.05);\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-url {\\n text-decoration: underline;\\n color: #027BFF;\\n cursor: pointer;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-bracket {\\n color: #9494FF;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-key {\\n color: #23A0DB;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler-link {\\n cursor: pointer;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler {\\n line-height: 1.2rem;\\n font-size: 0.7rem;\\n vertical-align: middle;\\n opacity: 0.6;\\n cursor: pointer;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler:after {\\n display: inline-block;\\n transition: transform 100ms ease-in;\\n content: \\\"\\\\25BA\\\";\\n}\\n.json-formatter-dark.json-formatter-row > a > .json-formatter-preview-text {\\n opacity: 0;\\n transition: opacity 0.15s ease-in;\\n font-style: italic;\\n}\\n.json-formatter-dark.json-formatter-row:hover > a > .json-formatter-preview-text {\\n opacity: 0.6;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > .json-formatter-toggler-link .json-formatter-toggler:after {\\n transform: rotate(90deg);\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > .json-formatter-children:after {\\n display: inline-block;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > a > .json-formatter-preview-text {\\n display: none;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open.json-formatter-empty:after {\\n display: block;\\n}\\n\");\n", - " },\n", - " function(Bokeh) {\n", - " inject_raw_css(\".codehilite .hll { background-color: #ffffcc }\\n.codehilite { background: #f8f8f8; }\\n.codehilite .c { color: #408080; font-style: italic } /* Comment */\\n.codehilite .err { border: 1px solid #FF0000 } /* Error */\\n.codehilite .k { color: #008000; font-weight: bold } /* Keyword */\\n.codehilite .o { color: #666666 } /* Operator */\\n.codehilite .ch { color: #408080; font-style: italic } /* Comment.Hashbang */\\n.codehilite .cm { color: #408080; font-style: italic } /* Comment.Multiline */\\n.codehilite .cp { color: #BC7A00 } /* Comment.Preproc */\\n.codehilite .cpf { color: #408080; font-style: italic } /* Comment.PreprocFile */\\n.codehilite .c1 { color: #408080; font-style: italic } /* Comment.Single */\\n.codehilite .cs { color: #408080; font-style: italic } /* Comment.Special */\\n.codehilite .gd { color: #A00000 } /* Generic.Deleted */\\n.codehilite .ge { font-style: italic } /* Generic.Emph */\\n.codehilite .gr { color: #FF0000 } /* 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{ color: #BA2121 } /* Literal.String */\\n.codehilite .na { color: #7D9029 } /* Name.Attribute */\\n.codehilite .nb { color: #008000 } /* Name.Builtin */\\n.codehilite .nc { color: #0000FF; font-weight: bold } /* Name.Class */\\n.codehilite .no { color: #880000 } /* Name.Constant */\\n.codehilite .nd { color: #AA22FF } /* Name.Decorator */\\n.codehilite .ni { color: #999999; font-weight: bold } /* Name.Entity */\\n.codehilite .ne { color: #D2413A; font-weight: bold } /* Name.Exception */\\n.codehilite .nf { color: #0000FF } /* Name.Function */\\n.codehilite .nl { color: #A0A000 } /* Name.Label */\\n.codehilite .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */\\n.codehilite .nt { color: #008000; font-weight: bold } /* Name.Tag */\\n.codehilite .nv { color: #19177C } /* Name.Variable */\\n.codehilite .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */\\n.codehilite .w { color: #bbbbbb } /* Text.Whitespace */\\n.codehilite .mb { color: #666666 } /* 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.sr { color: #BB6688 } /* Literal.String.Regex */\\n.codehilite .s1 { color: #BA2121 } /* Literal.String.Single */\\n.codehilite .ss { color: #19177C } /* Literal.String.Symbol */\\n.codehilite .bp { color: #008000 } /* Name.Builtin.Pseudo */\\n.codehilite .fm { color: #0000FF } /* Name.Function.Magic */\\n.codehilite .vc { color: #19177C } /* Name.Variable.Class */\\n.codehilite .vg { color: #19177C } /* Name.Variable.Global */\\n.codehilite .vi { color: #19177C } /* Name.Variable.Instance */\\n.codehilite .vm { color: #19177C } /* Name.Variable.Magic */\\n.codehilite .il { color: #666666 } /* Literal.Number.Integer.Long */\\n\\n.markdown h1 { margin-block-start: 0.34em }\\n.markdown h2 { margin-block-start: 0.42em }\\n.markdown h3 { margin-block-start: 0.5em }\\n.markdown h4 { margin-block-start: 0.67em }\\n.markdown h5 { margin-block-start: 0.84em }\\n.markdown h6 { margin-block-start: 1.17em }\\n.markdown ul { padding-inline-start: 2em }\\n.markdown ol { padding-inline-start: 2em }\\n.markdown strong { font-weight: 600 }\\n.markdown a { color: -webkit-link }\\n.markdown a { color: -moz-hyperlinkText }\\n\");\n", - " },\n", - " function(Bokeh) {\n", - " inject_raw_css(\"table.panel-df {\\n margin-left: auto;\\n margin-right: auto;\\n border: none;\\n border-collapse: collapse;\\n border-spacing: 0;\\n color: black;\\n font-size: 12px;\\n table-layout: fixed;\\n width: 100%;\\n}\\n\\n.panel-df tr, th, td {\\n text-align: right;\\n vertical-align: middle;\\n padding: 0.5em 0.5em !important;\\n line-height: normal;\\n white-space: normal;\\n max-width: none;\\n border: none;\\n}\\n\\n.panel-df tbody {\\n display: table-row-group;\\n vertical-align: middle;\\n border-color: inherit;\\n}\\n\\n.panel-df tbody tr:nth-child(odd) {\\n background: #f5f5f5;\\n}\\n\\n.panel-df thead {\\n border-bottom: 1px solid black;\\n vertical-align: bottom;\\n}\\n\\n.panel-df tr:hover {\\n background: lightblue !important;\\n cursor: pointer;\\n}\\n\");\n", - " },\n", - " function(Bokeh) {\n", - " Bokeh.set_log_level(\"info\");\n", - " },\n", - " \n", - " function(Bokeh) {\n", - " /* BEGIN panel.min.js */\n", - " /*!\n", - " * Copyright (c) 2012 - 2019, Anaconda, Inc., and Bokeh Contributors\n", - " * All rights reserved.\n", - " * \n", - " * Redistribution and use in source and binary forms, with or without modification,\n", - " * are permitted provided that the following conditions are met:\n", - " * \n", - " * Redistributions of source code must retain the above copyright notice,\n", - " * this list of conditions and the following disclaimer.\n", - " * \n", - " * Redistributions in binary form must reproduce the above copyright notice,\n", - " * this list of conditions and the following disclaimer in the documentation\n", - " * and/or other materials provided with the distribution.\n", - " * \n", - " * Neither the name of Anaconda nor the names of any contributors\n", - " * may be used to endorse or promote products derived from this software\n", - " * without specific prior written permission.\n", - " * \n", - " * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\n", - " * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\n", - " * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE\n", - " * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE\n", - " * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR\n", - " * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF\n", - " * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS\n", - " * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN\n", - " * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)\n", - " * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF\n", - " * THE POSSIBILITY OF SUCH DAMAGE.\n", - " */\n", - " (function(root, factory) {\n", - " factory(root[\"Bokeh\"]);\n", - " })(this, function(Bokeh) {\n", - " var define;\n", - " return (function(modules, entry, aliases, externals) {\n", - " if (Bokeh != null) {\n", - " return Bokeh.register_plugin(modules, entry, aliases, externals);\n", - " } else {\n", - " throw new Error(\"Cannot find Bokeh. You have to load it prior to loading plugins.\");\n", - " }\n", - " })\n", - " ({\n", - " \"aa4f566620\": function _(r,e,t){var n=(this&&this.__importStar||function(r){if(r&&r.__esModule)return r;var e={};if(null!=r)for(var t in r)Object.hasOwnProperty.call(r,t)&&(e[t]=r[t]);return e.default=r,e})(r(\"4d02676c49\"));t.Panel=n,r(\"@bokehjs/base\").register_models(n)},\n", - " \"4d02676c49\": function _(a,e,r){var o=a(\"ff4b91e885\");r.AcePlot=o.AcePlot;var t=a(\"12e90a1b7e\");r.Audio=t.Audio;var c=a(\"cf3b018c7a\");r.DeckGLPlot=c.DeckGLPlot;var d=a(\"70a2bb70ef\");r.HTML=d.HTML;var v=a(\"dac8d750fa\");r.JSON=v.JSON;var P=a(\"c81021c8fd\");r.KaTeX=P.KaTeX;var b=a(\"a93ded647d\");r.MathJax=b.MathJax;var l=a(\"98100899bc\");r.Player=l.Player;var f=a(\"d46f026c83\");r.PlotlyPlot=f.PlotlyPlot;var i=a(\"d9b3a262de\");r.Progress=i.Progress;var n=a(\"4b4afba86a\");r.State=n.State;var S=a(\"14b669e6fc\");r.VegaPlot=S.VegaPlot;var V=a(\"71a2bbec38\");r.Video=V.Video;var 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e=this;t.prototype.render.call(this),this.audioEl=document.createElement(\"audio\"),this.audioEl.controls=!0,this.audioEl.src=this.model.value,this.audioEl.currentTime=this.model.time,this.audioEl.loop=this.model.loop,null!=this.model.volume?this.audioEl.volume=this.model.volume/100:this.model.volume=100*this.audioEl.volume,this.audioEl.onpause=function(){return e.model.paused=!0},this.audioEl.onplay=function(){return e.model.paused=!1},this.audioEl.ontimeupdate=function(){return e.update_time(e)},this.audioEl.onvolumechange=function(){return e.update_volume(e)},this.el.appendChild(this.audioEl),this.model.paused||this.audioEl.play()},e.prototype.update_time=function(t){t._setting?t._setting=!1:Date.now()-t._time1&&\"number\"==typeof h[0]?l[u]=r.data[u].slice(c*h[1],c*h[1]+h[1]):l[u]=r.data[u][c]}a.push(l)}i.data=a}t&&this.updateDeck()},e.prototype._on_click_event=function(t){var 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e.html?n.html=p(e.html,t.object):n.text=p(e.text,t.object),n}:o:null}},\n", - " \"093eb75864\": function 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t={};if(null!=e)for(var n in e)Object.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t})(e(\"@bokehjs/core/properties\")),a=e(\"@bokehjs/core/dom\"),s=e(\"7620c2cc05\"),c=e(\"3b847a648d\"),d=function(e){function t(){var t=null!==e&&e.apply(this,arguments)||this;return t._axes_initialized=!1,t}return o(t,e),t.prototype.connect_signals=function(){var t=this;e.prototype.connect_signals.call(this),this.connect(this.model.properties.axes.change,function(){t._delete_axes(),t.model.axes&&t._set_axes(),t._vtk_renwin.getRenderWindow().render()}),this.el.addEventListener(\"mouseenter\",function(){var e=t._vtk_renwin.getInteractor();t.model.enable_keybindings&&(document.querySelector(\"body\").addEventListener(\"keypress\",e.handleKeyPress),document.querySelector(\"body\").addEventListener(\"keydown\",e.handleKeyDown),document.querySelector(\"body\").addEventListener(\"keyup\",e.handleKeyUp))}),this.el.addEventListener(\"mouseleave\",function(){var e=t._vtk_renwin.getInteractor();document.querySelector(\"body\").removeEventListener(\"keypress\",e.handleKeyPress),document.querySelector(\"body\").removeEventListener(\"keydown\",e.handleKeyDown),document.querySelector(\"body\").removeEventListener(\"keyup\",e.handleKeyUp)})},t.prototype.render=function(){e.prototype.render.call(this),this._axes=null,this._axes_initialized=!1,this._plot()},t.prototype.after_layout=function(){this._axes_initialized||(this._render_axes_canvas(),this._axes_initialized=!0)},t.prototype._render_axes_canvas=function(){var e=this,t=this._vtk_container.getElementsByTagName(\"canvas\");if(1!=t.length)throw Error(\"Error at initialization of the 3D scene, container should have one and only one canvas\");t[0].classList.add(\"scene3d-canvas\");var n=a.canvas({style:{position:\"absolute\",top:\"0\",left:\"0\",width:\"100%\",height:\"100%\"}});n.classList.add(\"axes-canvas\"),this._vtk_container.appendChild(n),this._vtk_renwin.setResizeCallback(function(){var t=e._vtk_container.getBoundingClientRect(),i=Math.floor(t.width*window.devicePixelRatio),o=Math.floor(t.height*window.devicePixelRatio);n.setAttribute(\"width\",i.toFixed()),n.setAttribute(\"height\",o.toFixed())})},t.prototype._delete_axes=function(){var e=this;if(null!=this._axes){Object.keys(this._axes).forEach(function(t){return e._vtk_renwin.getRenderer().removeActor(e._axes[t])});var t=this._vtk_renwin.getContainer().getElementsByClassName(\"axes-canvas\")[0],n=t.getContext(\"2d\");n&&n.clearRect(0,0,t.clientWidth*window.devicePixelRatio,t.clientHeight*window.devicePixelRatio),this._axes=null}},t.prototype._set_axes=function(){if(this.model.axes){var e=this._vtk_renwin.getContainer().getElementsByClassName(\"axes-canvas\")[0],t=this.model.axes.create_axes(e),n=t.psActor,i=t.axesActor,o=t.gridActor;this._axes={psActor:n,axesActor:i,gridActor:o},this._vtk_renwin.getRenderer().addActor(n),this._vtk_renwin.getRenderer().addActor(i),this._vtk_renwin.getRenderer().addActor(o)}},t.prototype._plot=function(){var e=this;if(this.model.data)var t=c.vtkns.DataAccessHelper.get(\"zip\",{zipContent:atob(this.model.data),callback:function(n){var i=c.vtkns.HttpSceneLoader.newInstance({renderer:e._vtk_renwin.getRenderer(),dataAccessHelper:t}),o=c.vtk.macro.debounce(function(){null==e._axes&&e.model.axes&&e._set_axes(),e.model.properties.camera.change.emit()},100);i.setUrl(\"index.json\"),i.onReady(o)}});else this._vtk_renwin.getRenderWindow().render()},t.__name__=\"VTKPlotView\",t}(s.AbstractVTKView);n.VTKPlotView=d;var l=function(e){function t(t){var n=e.call(this,t)||this;n.outline=c.vtkns.OutlineFilter.newInstance();var i=c.vtkns.Mapper.newInstance();return i.setInputConnection(n.outline.getOutputPort()),n.outline_actor=c.vtkns.Actor.newInstance(),n.outline_actor.setMapper(i),n}return o(t,e),t.init_VTKPlot=function(){this.prototype.default_view=d,this.define({data:[r.String],axes:[r.Instance],enable_keybindings:[r.Boolean,!1]})},t.__name__=\"VTKPlot\",t}(s.AbstractVTKPlot);n.VTKPlot=l,l.init_VTKPlot()},\n", - " \"7620c2cc05\": function _(e,t,n){var i,r=this&&this.__extends||(i=function(e,t){return(i=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(e,t){e.__proto__=t}||function(e,t){for(var n in t)t.hasOwnProperty(n)&&(e[n]=t[n])})(e,t)},function(e,t){function n(){this.constructor=e}i(e,t),e.prototype=null===t?Object.create(t):(n.prototype=t.prototype,new n)}),o=(this&&this.__importStar||function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t})(e(\"@bokehjs/core/properties\")),a=e(\"@bokehjs/core/dom\"),s=e(\"@bokehjs/core/util/object\"),_=e(\"@bokehjs/models/layouts/html_box\"),c=e(\"ec60963462\"),d=e(\"3b847a648d\"),h=function(e){function t(){var t=null!==e&&e.apply(this,arguments)||this;return t._setting_camera=!1,t}return r(t,e),t.prototype.connect_signals=function(){var t=this;e.prototype.connect_signals.call(this),this.connect(this.model.properties.data.change,function(){t.invalidate_render()}),this.connect(this.model.properties.orientation_widget.change,function(){t._orientation_widget_visibility(t.model.orientation_widget)}),this.connect(this.model.properties.camera.change,function(){return t._set_camera_state()})},t.prototype._orientation_widget_visibility=function(e){this._orientationWidget.setEnabled(e),e?this._widgetManager.enablePicking():this._widgetManager.disablePicking(),this._orientationWidget.updateMarkerOrientation(),this._vtk_renwin.getRenderWindow().render()},t.prototype._create_orientation_widget=function(){var e=this,t=d.vtkns.AxesActor.newInstance(),n=d.vtkns.OrientationMarkerWidget.newInstance({actor:t,interactor:this._vtk_renwin.getInteractor()});n.setEnabled(!0),n.setViewportCorner(d.vtkns.OrientationMarkerWidget.Corners.BOTTOM_RIGHT),n.setViewportSize(.15),n.setMinPixelSize(100),n.setMaxPixelSize(300),this._orientationWidget=n;var i=d.vtkns.WidgetManager.newInstance();i.setRenderer(n.getRenderer());var r=d.vtkns.InteractiveOrientationWidget.newInstance();r.placeWidget(t.getBounds()),r.setBounds(t.getBounds()),r.setPlaceFactor(1);var o=i.addWidget(r);this._widgetManager=i,o.onOrientationChange(function(t){var n=t.direction,i=e._vtk_renwin.getRenderer().getActiveCamera(),r=i.getFocalPoint(),o=i.getPosition(),a=i.getViewUp(),s=Math.sqrt(Math.pow(o[0]-r[0],2)+Math.pow(o[1]-r[1],2)+Math.pow(o[2]-r[2],2));i.setPosition(r[0]+n[0]*s,r[1]+n[1]*s,r[2]+n[2]*s),n[0]&&i.setViewUp(d.majorAxis(a,1,2)),n[1]&&i.setViewUp(d.majorAxis(a,0,2)),n[2]&&i.setViewUp(d.majorAxis(a,0,1)),e._orientationWidget.updateMarkerOrientation(),e._vtk_renwin.getRenderer().resetCameraClippingRange(),e._vtk_renwin.getRenderWindow().render()}),this._orientation_widget_visibility(this.model.orientation_widget)},t.prototype._get_camera_state=function(){if(!this._setting_camera){this._setting_camera=!0;var e=s.clone(this._vtk_renwin.getRenderer().getActiveCamera().get());delete e.classHierarchy,delete e.vtkObject,delete e.vtkCamera,delete e.viewPlaneNormal,this.model.camera=e,this._setting_camera=!1}},t.prototype._set_camera_state=function(){if(!this._setting_camera){this._setting_camera=!0;try{this.model.camera&&this._vtk_renwin.getRenderer().getActiveCamera().set(this.model.camera)}finally{this._setting_camera=!1}this._orientationWidget.updateMarkerOrientation(),this._vtk_renwin.getRenderer().resetCameraClippingRange(),this._vtk_renwin.getRenderWindow().render()}},t.prototype.render=function(){var t=this;e.prototype.render.call(this),this._orientationWidget=null,this._vtk_container=a.div(),c.set_size(this._vtk_container,this.model),this.el.appendChild(this._vtk_container),this._vtk_renwin=d.vtkns.FullScreenRenderWindow.newInstance({rootContainer:this.el,container:this._vtk_container}),this._remove_default_key_binding(),this._create_orientation_widget(),this._vtk_renwin.getRenderer().getActiveCamera().onModified(function(){return t._get_camera_state()}),this._set_camera_state(),this.model.renderer_el=this._vtk_renwin},t.prototype.after_layout=function(){e.prototype.after_layout.call(this),this._vtk_renwin.resize()},t.prototype._remove_default_key_binding=function(){var e=this._vtk_renwin.getInteractor();document.querySelector(\"body\").removeEventListener(\"keypress\",e.handleKeyPress),document.querySelector(\"body\").removeEventListener(\"keydown\",e.handleKeyDown),document.querySelector(\"body\").removeEventListener(\"keyup\",e.handleKeyUp)},t.__name__=\"AbstractVTKView\",t}(c.PanelHTMLBoxView);n.AbstractVTKView=h;var l=function(e){function t(t){return e.call(this,t)||this}return r(t,e),t.prototype.getActors=function(){return this.renderer_el.getRenderer().getActors()},t.init_AbstractVTKPlot=function(){this.define({orientation_widget:[o.Boolean,!1],camera:[o.Instance]}),this.override({height:300,width:300})},t.__name__=\"AbstractVTKPlot\",t.__module__=\"panel.models.vtk\",t}(_.HTMLBox);n.AbstractVTKPlot=l,l.init_AbstractVTKPlot()},\n", - " \"3b847a648d\": function _(e,t,n){var r=e(\"@bokehjs/core/util/serialization\"),a=e(\"@bokehjs/core/util/array\");function o(e){var t=Math.min(Math.max(Math.round(e),0),255).toString(16);return 2==t.length?t:\"0\"+t}function i(e,t,n){return\"#\"+o(e)+o(t)+o(n)}function v(e){for(var t=new ArrayBuffer(e.length),n=new Uint8Array(t),r=0,a=e.length;rMath.abs(e[n])?t:n,o=e[a]>0?1:-1;return r[a]=o,r},n.cartesian_product=function(){for(var e=[],t=0;t=.005&&(e.model.sampling=t)}),Math.abs(this.model.sampling-Number(this.shadow_selector.value))>=.005&&this.model.properties.sampling.change.emit(),this.edge_gradient_slider.addEventListener(\"input\",function(){var t=Number(e.edge_gradient_slider.value);Math.abs(e.model.edge_gradient-t)>=.005&&(e.model.edge_gradient=t)}),Math.abs(this.model.edge_gradient-Number(this.edge_gradient_slider.value))>=.005&&this.model.properties.edge_gradient.change.emit()},t.prototype._plot_volume=function(){var e=this,t=this._vtk_image_data,n=a.vtkns.Volume.newInstance(),r=a.vtkns.VolumeMapper.newInstance();n.setMapper(r),r.setInputData(t);var i=(t.getPointData().getScalars()||t.getPointData().getArrays()[0]).getRange(),o=a.vtkns.ColorTransferFunction.newInstance();o.onModified(function(){return e.model.mapper=a.vtkLutToMapper(o)});var s=a.vtkns.PiecewiseFunction.newInstance(),l=.7*Math.sqrt(t.getSpacing().map(function(e){return e*e}).reduce(function(e,t){return e+t},0));r.setSampleDistance(l),n.getProperty().setRGBTransferFunction(0,o),n.getProperty().setScalarOpacity(0,s),n.getProperty().setInterpolationTypeToFastLinear(),n.getProperty().setScalarOpacityUnitDistance(0,a.vtkns.BoundingBox.getDiagonalLength(t.getBounds())/Math.max.apply(Math,t.getDimensions())),n.getProperty().setGradientOpacityMinimumValue(0,0),n.getProperty().setGradientOpacityMaximumValue(0,.05*(i[1]-i[0])),n.getProperty().setShade(this.model.shadow),n.getProperty().setUseGradientOpacity(0,!0),n.getProperty().setGradientOpacityMinimumOpacity(0,0),n.getProperty().setGradientOpacityMaximumOpacity(0,1),n.getProperty().setAmbient(this.model.ambient),n.getProperty().setDiffuse(this.model.diffuse),n.getProperty().setSpecular(this.model.specular),n.getProperty().setSpecularPower(this.model.specular_power),this._vtk_renwin.getRenderer().addVolume(n),this._controllerWidget.setupContent(this._vtk_renwin.getRenderWindow(),n,!0)},t.prototype._plot_slices=function(){var e=this._vtk_image_data,t=a.vtkns.ImageSlice.newInstance(),n=a.vtkns.ImageSlice.newInstance(),r=a.vtkns.ImageSlice.newInstance(),i=a.vtkns.ImageMapper.newInstance(),o=a.vtkns.ImageMapper.newInstance(),s=a.vtkns.ImageMapper.newInstance();i.setInputData(e),i.setISlice(this.model.slice_i),t.setMapper(i),o.setInputData(e),o.setJSlice(this.model.slice_j),n.setMapper(o),s.setInputData(e),s.setKSlice(this.model.slice_k),r.setMapper(s);var l=a.vtkns.PiecewiseFunction.newInstance();l.removeAllPoints(),l.addPoint(0,1);var c=this.volume.getProperty().getRGBTransferFunction(0),p=t.getProperty();n.setProperty(p),r.setProperty(p),p.setRGBTransferFunction(c),p.setScalarOpacity(l);var d=this._vtk_renwin.getRenderer();d.addActor(t),d.addActor(n),d.addActor(r)},t.prototype._set_volume_visibility=function(e){this.volume.setVisibility(e)},t.prototype._set_slices_visibility=function(e){this._vtk_renwin.getRenderer().getActors().map(function(t){return t.setVisibility(e)})},t.__name__=\"VTKVolumePlotView\",t}(s.AbstractVTKView);n.VTKVolumePlotView=l;var c=function(e){function t(t){return e.call(this,t)||this}return i(t,e),t.init_VTKVolumePlot=function(){this.prototype.default_view=l,this.define({data:[o.Instance],shadow:[o.Boolean,!0],sampling:[o.Number,.4],edge_gradient:[o.Number,.2],colormap:[o.String],rescale:[o.Boolean,!1],ambient:[o.Number,.2],diffuse:[o.Number,.7],specular:[o.Number,.3],specular_power:[o.Number,8],slice_i:[o.Int,0],slice_j:[o.Int,0],slice_k:[o.Int,0],display_volume:[o.Boolean,!0],display_slices:[o.Boolean,!1],render_background:[o.String,\"#52576e\"],interpolation:[o.Any,\"fast_linear\"],mapper:[o.Instance]})},t.__name__=\"VTKVolumePlot\",t}(s.AbstractVTKPlot);n.VTKVolumePlot=c,c.init_VTKVolumePlot()},\n", - " \"5bc27423fe\": function _(t,e,i){var s,n=this&&this.__extends||(s=function(t,e){return(s=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var i in e)e.hasOwnProperty(i)&&(t[i]=e[i])})(t,e)},function(t,e){function i(){this.constructor=t}s(t,e),t.prototype=null===e?Object.create(e):(i.prototype=e.prototype,new i)}),r=this&&this.__importStar||function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var i in t)Object.hasOwnProperty.call(t,i)&&(e[i]=t[i]);return e.default=t,e},a=t(\"66e1dbda7d\"),c=t(\"@bokehjs/model\"),o=r(t(\"@bokehjs/core/properties\")),l=t(\"3b847a648d\"),h=function(t){function e(e){return t.call(this,e)||this}return n(e,t),e.init_VTKAxes=function(){this.define({origin:[o.Array],xticker:[o.Instance],yticker:[o.Instance],zticker:[o.Instance],digits:[o.Number,1],show_grid:[o.Boolean,!0],grid_opacity:[o.Number,.1],axes_opacity:[o.Number,1],fontsize:[o.Number,12]})},Object.defineProperty(e.prototype,\"xticks\",{get:function(){return this.xticker.ticks},enumerable:!0,configurable:!0}),Object.defineProperty(e.prototype,\"yticks\",{get:function(){return this.yticker.ticks},enumerable:!0,configurable:!0}),Object.defineProperty(e.prototype,\"zticks\",{get:function(){return this.zticker.ticks},enumerable:!0,configurable:!0}),Object.defineProperty(e.prototype,\"xlabels\",{get:function(){var t=this;return this.xticker.labels?this.xticker.labels:this.xticks.map(function(e){return e.toFixed(t.digits)})},enumerable:!0,configurable:!0}),Object.defineProperty(e.prototype,\"ylabels\",{get:function(){var t=this;return this.yticker.labels?this.yticker.labels:this.yticks.map(function(e){return e.toFixed(t.digits)})},enumerable:!0,configurable:!0}),Object.defineProperty(e.prototype,\"zlabels\",{get:function(){var t=this;return this.zticker.labels?this.zticker.labels:this.zticks.map(function(e){return e.toFixed(t.digits)})},enumerable:!0,configurable:!0}),e.prototype._make_grid_lines=function(t,e,i){for(var s=[],n=0;n=e.xticks.length&&i0?(n[0]=2*(M*h+c*r+s*u-f*e)/b,n[1]=2*(s*h+c*e+f*r-M*u)/b,n[2]=2*(f*h+c*u+M*e-s*r)/b):(n[0]=2*(M*h+c*r+s*u-f*e),n[1]=2*(s*h+c*e+f*r-M*u),n[2]=2*(f*h+c*u+M*e-s*r));return i(t,a,n),t},n.getTranslation=function(t,a){return t[0]=a[12],t[1]=a[13],t[2]=a[14],t},n.getScaling=M,n.getRotation=function(t,a){var n=new o.ARRAY_TYPE(3);M(n,a);var r=1/n[0],e=1/n[1],u=1/n[2],h=a[0]*r,i=a[1]*e,s=a[2]*u,f=a[4]*r,c=a[5]*e,b=a[6]*u,l=a[8]*r,v=a[9]*e,m=a[10]*u,p=h+c+m,y=0;p>0?(y=2*Math.sqrt(p+1),t[3]=.25*y,t[0]=(b-v)/y,t[1]=(l-s)/y,t[2]=(i-f)/y):h>c&&h>m?(y=2*Math.sqrt(1+h-c-m),t[3]=(b-v)/y,t[0]=.25*y,t[1]=(i+f)/y,t[2]=(l+s)/y):c>m?(y=2*Math.sqrt(1+c-h-m),t[3]=(l-s)/y,t[0]=(i+f)/y,t[1]=.25*y,t[2]=(b+v)/y):(y=2*Math.sqrt(1+m-h-c),t[3]=(i-f)/y,t[0]=(l+s)/y,t[1]=(b+v)/y,t[2]=.25*y);return t},n.fromRotationTranslationScale=function(t,a,n,r){var o=a[0],e=a[1],u=a[2],h=a[3],i=o+o,M=e+e,s=u+u,f=o*i,c=o*M,b=o*s,l=e*M,v=e*s,m=u*s,p=h*i,y=h*M,P=h*s,S=r[0],O=r[1],E=r[2];return t[0]=(1-(l+m))*S,t[1]=(c+P)*S,t[2]=(b-y)*S,t[3]=0,t[4]=(c-P)*O,t[5]=(1-(f+m))*O,t[6]=(v+p)*O,t[7]=0,t[8]=(b+y)*E,t[9]=(v-p)*E,t[10]=(1-(f+l))*E,t[11]=0,t[12]=n[0],t[13]=n[1],t[14]=n[2],t[15]=1,t},n.fromRotationTranslationScaleOrigin=function(t,a,n,r,o){var e=a[0],u=a[1],h=a[2],i=a[3],M=e+e,s=u+u,f=h+h,c=e*M,b=e*s,l=e*f,v=u*s,m=u*f,p=h*f,y=i*M,P=i*s,S=i*f,O=r[0],E=r[1],I=r[2],L=o[0],N=o[1],R=o[2],x=(1-(v+p))*O,d=(b+S)*O,g=(l-P)*O,A=(b-S)*E,Y=(1-(c+p))*E,T=(m+y)*E,w=(l+P)*I,_=(m-y)*I,q=(1-(c+v))*I;return t[0]=x,t[1]=d,t[2]=g,t[3]=0,t[4]=A,t[5]=Y,t[6]=T,t[7]=0,t[8]=w,t[9]=_,t[10]=q,t[11]=0,t[12]=n[0]+L-(x*L+A*N+w*R),t[13]=n[1]+N-(d*L+Y*N+_*R),t[14]=n[2]+R-(g*L+T*N+q*R),t[15]=1,t},n.fromQuat=function(t,a){var n=a[0],r=a[1],o=a[2],e=a[3],u=n+n,h=r+r,i=o+o,M=n*u,s=r*u,f=r*h,c=o*u,b=o*h,l=o*i,v=e*u,m=e*h,p=e*i;return 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\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"
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    • \\n\"+\n \"
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infinite;\\n}\\n\\nprogress.active:not([value])::-webkit-progress-bar {\\n\\tbackground-position: 10%;\\n\\tanimation-name: stripes;\\n\\tanimation-duration: 3s;\\n\\tanimation-timing-function: linear;\\n\\tanimation-iteration-count: infinite;\\n}\\n\\nprogress.primary[value]::-webkit-progress-value { background-color: #007bff; }\\nprogress.primary:not([value])::before { background-color: #007bff; }\\nprogress.primary:not([value])::-webkit-progress-bar { background-color: #007bff; }\\nprogress.primary::-moz-progress-bar { background-color: #007bff; }\\n\\nprogress.secondary[value]::-webkit-progress-value { background-color: #6c757d; }\\nprogress.secondary:not([value])::before { background-color: #6c757d; }\\nprogress.secondary:not([value])::-webkit-progress-bar { background-color: #6c757d; }\\nprogress.secondary::-moz-progress-bar { background-color: #6c757d; }\\n\\nprogress.success[value]::-webkit-progress-value { background-color: #28a745; }\\nprogress.success:not([value])::before { background-color: #28a745; }\\nprogress.success:not([value])::-webkit-progress-bar { background-color: #28a745; }\\nprogress.success::-moz-progress-bar { background-color: #28a745; }\\n\\nprogress.danger[value]::-webkit-progress-value { background-color: #dc3545; }\\nprogress.danger:not([value])::before { background-color: #dc3545; }\\nprogress.danger:not([value])::-webkit-progress-bar { background-color: #dc3545; }\\nprogress.danger::-moz-progress-bar { background-color: #dc3545; }\\n\\nprogress.warning[value]::-webkit-progress-value { background-color: #ffc107; }\\nprogress.warning:not([value])::before { background-color: #ffc107; }\\nprogress.warning:not([value])::-webkit-progress-bar { background-color: #ffc107; }\\nprogress.warning::-moz-progress-bar { background-color: #ffc107; }\\n\\nprogress.info[value]::-webkit-progress-value { background-color: #17a2b8; }\\nprogress.info:not([value])::before { background-color: #17a2b8; }\\nprogress.info:not([value])::-webkit-progress-bar { background-color: #17a2b8; }\\nprogress.info::-moz-progress-bar { background-color: #17a2b8; }\\n\\nprogress.light[value]::-webkit-progress-value { background-color: #f8f9fa; }\\nprogress.light:not([value])::before { background-color: #f8f9fa; }\\nprogress.light:not([value])::-webkit-progress-bar { background-color: #f8f9fa; }\\nprogress.light::-moz-progress-bar { background-color: #f8f9fa; }\\n\\nprogress.dark[value]::-webkit-progress-value { background-color: #343a40; }\\nprogress.dark:not([value])::-webkit-progress-bar { background-color: #343a40; }\\nprogress.dark:not([value])::before { background-color: #343a40; }\\nprogress.dark::-moz-progress-bar { background-color: #343a40; }\\n\\nprogress:not([value])::-webkit-progress-bar {\\n\\tborder-radius: 3px;\\n\\tbackground:\\n\\tlinear-gradient(-45deg, transparent 33%, rgba(0, 0, 0, 0.2) 33%, rgba(0, 0, 0, 0.2) 66%, transparent 66%) left/2.5em 1.5em;\\n}\\nprogress:not([value])::before {\\n\\tcontent:\\\" \\\";\\n\\tposition:absolute;\\n\\theight: 20px;\\n\\ttop:0;\\n\\tleft:0;\\n\\tright:0;\\n\\tbottom:0;\\n\\tborder-radius: 3px;\\n\\tbackground:\\n\\tlinear-gradient(-45deg, transparent 33%, rgba(0, 0, 0, 0.2) 33%, rgba(0, 0, 0, 0.2) 66%, transparent 66%) left/2.5em 1.5em;\\n}\\n\\n@keyframes stripes {\\n from {background-position: 0%}\\n to {background-position: 100%}\\n}\");\n },\n function(Bokeh) {\n inject_raw_css(\".json-formatter-row {\\n font-family: monospace;\\n}\\n.json-formatter-row,\\n.json-formatter-row a,\\n.json-formatter-row a:hover {\\n color: black;\\n text-decoration: none;\\n}\\n.json-formatter-row .json-formatter-row {\\n margin-left: 1rem;\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty {\\n opacity: 0.5;\\n margin-left: 1rem;\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty:after {\\n display: none;\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-object:after {\\n content: \\\"No properties\\\";\\n}\\n.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-array:after {\\n content: \\\"[]\\\";\\n}\\n.json-formatter-row .json-formatter-string,\\n.json-formatter-row .json-formatter-stringifiable {\\n color: green;\\n white-space: pre;\\n word-wrap: break-word;\\n}\\n.json-formatter-row .json-formatter-number {\\n color: blue;\\n}\\n.json-formatter-row .json-formatter-boolean {\\n color: red;\\n}\\n.json-formatter-row .json-formatter-null {\\n color: #855A00;\\n}\\n.json-formatter-row .json-formatter-undefined {\\n color: #ca0b69;\\n}\\n.json-formatter-row .json-formatter-function {\\n color: #FF20ED;\\n}\\n.json-formatter-row .json-formatter-date {\\n background-color: rgba(0, 0, 0, 0.05);\\n}\\n.json-formatter-row .json-formatter-url {\\n text-decoration: underline;\\n color: blue;\\n cursor: pointer;\\n}\\n.json-formatter-row .json-formatter-bracket {\\n color: blue;\\n}\\n.json-formatter-row .json-formatter-key {\\n color: #00008B;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-row .json-formatter-toggler-link {\\n cursor: pointer;\\n}\\n.json-formatter-row .json-formatter-toggler {\\n line-height: 1.2rem;\\n font-size: 0.7rem;\\n vertical-align: middle;\\n opacity: 0.6;\\n cursor: pointer;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-row .json-formatter-toggler:after {\\n display: inline-block;\\n transition: transform 100ms ease-in;\\n content: \\\"\\\\25BA\\\";\\n}\\n.json-formatter-row > a > .json-formatter-preview-text {\\n opacity: 0;\\n transition: opacity 0.15s ease-in;\\n font-style: italic;\\n}\\n.json-formatter-row:hover > a > .json-formatter-preview-text {\\n opacity: 0.6;\\n}\\n.json-formatter-row.json-formatter-open > .json-formatter-toggler-link .json-formatter-toggler:after {\\n transform: rotate(90deg);\\n}\\n.json-formatter-row.json-formatter-open > .json-formatter-children:after {\\n display: inline-block;\\n}\\n.json-formatter-row.json-formatter-open > a > .json-formatter-preview-text {\\n display: none;\\n}\\n.json-formatter-row.json-formatter-open.json-formatter-empty:after {\\n display: block;\\n}\\n.json-formatter-dark.json-formatter-row {\\n font-family: monospace;\\n}\\n.json-formatter-dark.json-formatter-row,\\n.json-formatter-dark.json-formatter-row a,\\n.json-formatter-dark.json-formatter-row a:hover {\\n color: white;\\n text-decoration: none;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-row {\\n margin-left: 1rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty {\\n opacity: 0.5;\\n margin-left: 1rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty:after {\\n display: none;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-object:after {\\n content: \\\"No properties\\\";\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-array:after {\\n content: \\\"[]\\\";\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-string,\\n.json-formatter-dark.json-formatter-row .json-formatter-stringifiable {\\n color: #31F031;\\n white-space: pre;\\n word-wrap: break-word;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-number {\\n color: #66C2FF;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-boolean {\\n color: #EC4242;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-null {\\n color: #EEC97D;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-undefined {\\n color: #ef8fbe;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-function {\\n color: #FD48CB;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-date {\\n background-color: rgba(255, 255, 255, 0.05);\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-url {\\n text-decoration: underline;\\n color: #027BFF;\\n cursor: pointer;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-bracket {\\n color: #9494FF;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-key {\\n color: #23A0DB;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler-link {\\n cursor: pointer;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler {\\n line-height: 1.2rem;\\n font-size: 0.7rem;\\n vertical-align: middle;\\n opacity: 0.6;\\n cursor: pointer;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler:after {\\n display: inline-block;\\n transition: transform 100ms ease-in;\\n content: \\\"\\\\25BA\\\";\\n}\\n.json-formatter-dark.json-formatter-row > a > .json-formatter-preview-text {\\n opacity: 0;\\n transition: opacity 0.15s ease-in;\\n font-style: italic;\\n}\\n.json-formatter-dark.json-formatter-row:hover > a > .json-formatter-preview-text {\\n opacity: 0.6;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > .json-formatter-toggler-link .json-formatter-toggler:after {\\n transform: rotate(90deg);\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > .json-formatter-children:after {\\n display: inline-block;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > a > .json-formatter-preview-text {\\n display: none;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open.json-formatter-empty:after {\\n display: block;\\n}\\n\");\n },\n function(Bokeh) {\n inject_raw_css(\".codehilite .hll { background-color: #ffffcc }\\n.codehilite { background: #f8f8f8; }\\n.codehilite .c { color: #408080; font-style: italic } /* Comment */\\n.codehilite .err { border: 1px solid #FF0000 } /* Error */\\n.codehilite .k { color: #008000; font-weight: bold } /* Keyword */\\n.codehilite .o { color: #666666 } /* Operator */\\n.codehilite .ch { color: #408080; font-style: italic } /* Comment.Hashbang */\\n.codehilite .cm { color: #408080; font-style: italic } /* Comment.Multiline */\\n.codehilite .cp { color: #BC7A00 } /* Comment.Preproc */\\n.codehilite .cpf { color: #408080; font-style: italic } /* Comment.PreprocFile */\\n.codehilite .c1 { color: #408080; font-style: italic } /* Comment.Single */\\n.codehilite .cs { color: #408080; font-style: italic } /* Comment.Special */\\n.codehilite .gd { color: #A00000 } /* Generic.Deleted */\\n.codehilite .ge { font-style: italic } /* Generic.Emph */\\n.codehilite .gr { color: #FF0000 } /* Generic.Error */\\n.codehilite .gh { color: #000080; font-weight: bold } /* Generic.Heading */\\n.codehilite .gi { color: #00A000 } /* Generic.Inserted */\\n.codehilite .go { color: #888888 } /* Generic.Output */\\n.codehilite .gp { color: #000080; font-weight: bold } /* Generic.Prompt */\\n.codehilite .gs { font-weight: bold } /* Generic.Strong */\\n.codehilite .gu { color: #800080; font-weight: bold } /* Generic.Subheading */\\n.codehilite .gt { color: #0044DD } /* Generic.Traceback */\\n.codehilite .kc { color: #008000; font-weight: bold } /* Keyword.Constant */\\n.codehilite .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */\\n.codehilite .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */\\n.codehilite .kp { color: #008000 } /* Keyword.Pseudo */\\n.codehilite .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */\\n.codehilite .kt { color: #B00040 } /* Keyword.Type */\\n.codehilite .m { color: #666666 } /* Literal.Number */\\n.codehilite .s { color: #BA2121 } /* Literal.String */\\n.codehilite .na { color: #7D9029 } /* Name.Attribute */\\n.codehilite .nb { color: #008000 } /* Name.Builtin */\\n.codehilite .nc { color: #0000FF; font-weight: bold } /* Name.Class */\\n.codehilite .no { color: #880000 } /* Name.Constant */\\n.codehilite .nd { color: #AA22FF } /* Name.Decorator */\\n.codehilite .ni { color: #999999; font-weight: bold } /* Name.Entity */\\n.codehilite .ne { color: #D2413A; font-weight: bold } /* Name.Exception */\\n.codehilite .nf { color: #0000FF } /* Name.Function */\\n.codehilite .nl { color: #A0A000 } /* Name.Label */\\n.codehilite .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */\\n.codehilite .nt { color: #008000; font-weight: bold } /* Name.Tag */\\n.codehilite .nv { color: #19177C } /* Name.Variable */\\n.codehilite .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */\\n.codehilite .w { color: #bbbbbb } /* Text.Whitespace */\\n.codehilite .mb { color: #666666 } /* Literal.Number.Bin */\\n.codehilite .mf { color: #666666 } /* Literal.Number.Float */\\n.codehilite .mh { color: #666666 } /* Literal.Number.Hex */\\n.codehilite .mi { color: #666666 } /* Literal.Number.Integer */\\n.codehilite .mo { color: #666666 } /* Literal.Number.Oct */\\n.codehilite .sa { color: #BA2121 } /* Literal.String.Affix */\\n.codehilite .sb { color: #BA2121 } /* Literal.String.Backtick */\\n.codehilite .sc { color: #BA2121 } /* Literal.String.Char */\\n.codehilite .dl { color: #BA2121 } /* Literal.String.Delimiter */\\n.codehilite .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */\\n.codehilite .s2 { color: #BA2121 } /* Literal.String.Double */\\n.codehilite .se { color: #BB6622; font-weight: bold } /* Literal.String.Escape */\\n.codehilite .sh { color: #BA2121 } /* Literal.String.Heredoc */\\n.codehilite .si { color: #BB6688; font-weight: bold } /* Literal.String.Interpol */\\n.codehilite .sx { color: #008000 } /* Literal.String.Other */\\n.codehilite .sr { color: #BB6688 } /* Literal.String.Regex */\\n.codehilite .s1 { color: #BA2121 } /* Literal.String.Single */\\n.codehilite .ss { color: #19177C } /* Literal.String.Symbol */\\n.codehilite .bp { color: #008000 } /* Name.Builtin.Pseudo */\\n.codehilite .fm { color: #0000FF } /* Name.Function.Magic */\\n.codehilite .vc { color: #19177C } /* Name.Variable.Class */\\n.codehilite .vg { color: #19177C } /* Name.Variable.Global */\\n.codehilite .vi { color: #19177C } /* Name.Variable.Instance */\\n.codehilite .vm { color: #19177C } /* Name.Variable.Magic */\\n.codehilite .il { color: #666666 } /* Literal.Number.Integer.Long */\\n\\n.markdown h1 { margin-block-start: 0.34em }\\n.markdown h2 { margin-block-start: 0.42em }\\n.markdown h3 { margin-block-start: 0.5em }\\n.markdown h4 { margin-block-start: 0.67em }\\n.markdown h5 { margin-block-start: 0.84em }\\n.markdown h6 { margin-block-start: 1.17em }\\n.markdown ul { padding-inline-start: 2em }\\n.markdown ol { padding-inline-start: 2em }\\n.markdown strong { font-weight: 600 }\\n.markdown a { color: -webkit-link }\\n.markdown a { color: -moz-hyperlinkText }\\n\");\n },\n function(Bokeh) {\n inject_raw_css(\"table.panel-df {\\n margin-left: auto;\\n margin-right: auto;\\n border: none;\\n border-collapse: collapse;\\n border-spacing: 0;\\n color: black;\\n font-size: 12px;\\n table-layout: fixed;\\n width: 100%;\\n}\\n\\n.panel-df tr, th, td {\\n text-align: right;\\n vertical-align: middle;\\n padding: 0.5em 0.5em !important;\\n line-height: normal;\\n white-space: normal;\\n max-width: none;\\n border: none;\\n}\\n\\n.panel-df tbody {\\n display: table-row-group;\\n vertical-align: middle;\\n border-color: inherit;\\n}\\n\\n.panel-df tbody tr:nth-child(odd) {\\n background: #f5f5f5;\\n}\\n\\n.panel-df thead {\\n border-bottom: 1px solid black;\\n vertical-align: bottom;\\n}\\n\\n.panel-df tr:hover {\\n background: lightblue !important;\\n cursor: pointer;\\n}\\n\");\n },\n function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\n \n function(Bokeh) {\n /* BEGIN panel.min.js */\n /*!\n * Copyright (c) 2012 - 2019, Anaconda, Inc., and Bokeh Contributors\n * All rights reserved.\n * \n * Redistribution and use in source and binary forms, with or without modification,\n * are permitted provided that the following conditions are met:\n * \n * Redistributions of source code must retain the above copyright notice,\n * this list of conditions and the following disclaimer.\n * \n * Redistributions in binary form must reproduce the above copyright notice,\n * this list of conditions and the following disclaimer in the documentation\n * and/or other materials provided with the distribution.\n * \n * Neither the name of Anaconda nor the names of any contributors\n * may be used to endorse or promote products derived from this software\n * without specific prior written permission.\n * \n * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\n * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\n * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE\n * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE\n * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR\n * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF\n * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS\n * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN\n * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)\n * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF\n * THE POSSIBILITY OF SUCH DAMAGE.\n */\n (function(root, factory) {\n factory(root[\"Bokeh\"]);\n })(this, function(Bokeh) {\n var define;\n return (function(modules, entry, aliases, externals) {\n if (Bokeh != null) {\n return Bokeh.register_plugin(modules, entry, aliases, externals);\n } else {\n throw new Error(\"Cannot find Bokeh. You have to load it prior to loading plugins.\");\n }\n })\n ({\n \"aa4f566620\": function _(r,e,t){var n=(this&&this.__importStar||function(r){if(r&&r.__esModule)return r;var e={};if(null!=r)for(var t in r)Object.hasOwnProperty.call(r,t)&&(e[t]=r[t]);return e.default=r,e})(r(\"4d02676c49\"));t.Panel=n,r(\"@bokehjs/base\").register_models(n)},\n \"4d02676c49\": function _(a,e,r){var o=a(\"ff4b91e885\");r.AcePlot=o.AcePlot;var t=a(\"12e90a1b7e\");r.Audio=t.Audio;var c=a(\"cf3b018c7a\");r.DeckGLPlot=c.DeckGLPlot;var d=a(\"70a2bb70ef\");r.HTML=d.HTML;var v=a(\"dac8d750fa\");r.JSON=v.JSON;var P=a(\"c81021c8fd\");r.KaTeX=P.KaTeX;var b=a(\"a93ded647d\");r.MathJax=b.MathJax;var l=a(\"98100899bc\");r.Player=l.Player;var f=a(\"d46f026c83\");r.PlotlyPlot=f.PlotlyPlot;var i=a(\"d9b3a262de\");r.Progress=i.Progress;var n=a(\"4b4afba86a\");r.State=n.State;var S=a(\"14b669e6fc\");r.VegaPlot=S.VegaPlot;var V=a(\"71a2bbec38\");r.Video=V.Video;var s=a(\"76bc93d621\");r.VideoStream=s.VideoStream,function(a){for(var e in a)r.hasOwnProperty(e)||(r[e]=a[e])}(a(\"63070bc9ce\"))},\n \"ff4b91e885\": function _(t,e,o){var i,n=this&&this.__extends||(i=function(t,e){return(i=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var o in e)e.hasOwnProperty(o)&&(t[o]=e[o])})(t,e)},function(t,e){function o(){this.constructor=t}i(t,e),t.prototype=null===e?Object.create(e):(o.prototype=e.prototype,new o)}),r=(this&&this.__importStar||function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var o in t)Object.hasOwnProperty.call(t,o)&&(e[o]=t[o]);return e.default=t,e})(t(\"@bokehjs/core/properties\")),s=t(\"@bokehjs/models/layouts/html_box\"),a=t(\"@bokehjs/core/dom\");var c=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return n(e,t),e.prototype.initialize=function(){t.prototype.initialize.call(this),this._ace=window.ace,this._container=a.div({id:\"_\"+Math.random().toString(36).substr(2,9),style:{width:\"100%\",height:\"100%\"}})},e.prototype.connect_signals=function(){var e=this;t.prototype.connect_signals.call(this),this.connect(this.model.properties.code.change,function(){return e._update_code_from_model()}),this.connect(this.model.properties.theme.change,function(){return e._update_theme()}),this.connect(this.model.properties.language.change,function(){return e._update_language()}),this.connect(this.model.properties.annotations.change,function(){return e._add_annotations()}),this.connect(this.model.properties.readonly.change,function(){e._editor.setReadOnly(e.model.readonly)})},e.prototype.render=function(){var e=this;t.prototype.render.call(this),this._container!==this.el.childNodes[0]&&this.el.appendChild(this._container),this._container.textContent=this.model.code,this._editor=this._ace.edit(this._container.id),this._editor.setTheme(\"ace/theme/\"+this.model.theme),this._editor.session.setMode(\"ace/mode/\"+this.model.language),this._editor.setReadOnly(this.model.readonly),this._langTools=this._ace.require(\"ace/ext/language_tools\"),this._editor.setOptions({enableBasicAutocompletion:!0,enableSnippets:!0,fontFamily:\"monospace\"}),this._editor.on(\"change\",function(){return e._update_code_from_editor()})},e.prototype._update_code_from_model=function(){this._editor&&this._editor.getValue()!=this.model.code&&this._editor.setValue(this.model.code)},e.prototype._update_code_from_editor=function(){this._editor.getValue()!=this.model.code&&(this.model.code=this._editor.getValue())},e.prototype._update_theme=function(){this._editor.setTheme(\"ace/theme/\"+this.model.theme)},e.prototype._update_language=function(){this._editor.session.setMode(\"ace/mode/\"+this.model.language)},e.prototype._add_annotations=function(){this._editor.session.setAnnotations(this.model.annotations)},e.prototype.after_layout=function(){t.prototype.after_layout.call(this),this._editor.resize()},e.__name__=\"AcePlotView\",e}(t(\"ec60963462\").PanelHTMLBoxView);o.AcePlotView=c;var h=function(t){function e(e){return t.call(this,e)||this}return n(e,t),e.init_AcePlot=function(){this.prototype.default_view=c,this.define({code:[r.String],language:[r.String,\"python\"],theme:[r.String,\"chrome\"],annotations:[r.Array,[]],readonly:[r.Boolean,!1]}),this.override({height:300,width:300})},e.__name__=\"AcePlot\",e.__module__=\"panel.models.ace\",e}(s.HTMLBox);o.AcePlot=h,h.init_AcePlot()},\n \"ec60963462\": function _(e,t,i){var o,n=this&&this.__extends||(o=function(e,t){return(o=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(e,t){e.__proto__=t}||function(e,t){for(var i in t)t.hasOwnProperty(i)&&(e[i]=t[i])})(e,t)},function(e,t){function i(){this.constructor=e}o(e,t),e.prototype=null===t?Object.create(t):(i.prototype=t.prototype,new i)}),s=e(\"@bokehjs/core/layout/layoutable\"),h=e(\"@bokehjs/core/layout/types\"),r=e(\"@bokehjs/core/dom\"),a=e(\"@bokehjs/models/widgets/markup\"),_=e(\"@bokehjs/models/layouts/html_box\");function c(e,t){var i=null!=t.width?\"fixed\":\"fit\",o=null!=t.height?\"fixed\":\"fit\",n=t.sizing_mode;if(null!=n)if(\"fixed\"==n)i=o=\"fixed\";else if(\"stretch_both\"==n)i=o=\"max\";else if(\"stretch_width\"==n)i=\"max\";else if(\"stretch_height\"==n)o=\"max\";else switch(n){case\"scale_width\":i=\"max\",o=\"min\";break;case\"scale_height\":i=\"min\",o=\"max\";break;case\"scale_both\":i=\"max\",o=\"max\";break;default:throw new Error(\"unreachable\")}\"fixed\"==i&&t.width?e.style.width=t.width+\"px\":\"max\"==i&&(e.style.width=\"100%\"),\"fixed\"==o&&t.height?e.style.height=t.height+\"px\":\"max\"==o&&(e.style.height=\"100%\")}i.set_size=c;var l=function(e){function t(t,i,o){var n=e.call(this)||this;return n.el=t,n.sizing_mode=i,n.changed=o,n._cache={},n._cache_count={},n}return n(t,e),t.prototype._measure=function(e){var t=this,i=[e.width,e.height,this.sizing_mode].toString(),o=this.changed&&\"fixed\"!=this.sizing_mode&&null!=this.sizing_mode?1:0;if(i in this._cache&&this._cache_count[i]>=o)return this._cache_count[i]=this._cache_count[i]+1,this._cache[i];var n=new h.Sizeable(e).bounded_to(this.sizing.size),s=r.sized(this.el,n,function(){var e=new h.Sizeable(r.content_size(t.el)),i=r.extents(t.el),o=i.border,n=i.padding;return e.grow_by(o).grow_by(n).map(Math.ceil)});return this._cache[i]=s,this._cache_count[i]=0,s},t.__name__=\"CachedVariadicBox\",t}(s.Layoutable);i.CachedVariadicBox=l;var d=function(e){function t(){return null!==e&&e.apply(this,arguments)||this}return n(t,e),t.prototype._update_layout=function(){var e=void 0!==this._prev_sizing_mode&&this._prev_sizing_mode!==this.model.sizing_mode;this._prev_sizing_mode=this.model.sizing_mode,this.layout=new l(this.el,this.model.sizing_mode,e),this.layout.set_sizing(this.box_sizing())},t.prototype.render=function(){e.prototype.render.call(this),c(this.markup_el,this.model)},t.__name__=\"PanelMarkupView\",t}(a.MarkupView);i.PanelMarkupView=d;var u=function(e){function t(){return null!==e&&e.apply(this,arguments)||this}return n(t,e),t.prototype._update_layout=function(){var e=void 0!==this._prev_sizing_mode&&this._prev_sizing_mode!==this.model.sizing_mode;this._prev_sizing_mode=this.model.sizing_mode,this.layout=new l(this.el,this.model.sizing_mode,e),this.layout.set_sizing(this.box_sizing())},t.prototype.render=function(){e.prototype.render.call(this),c(this.el,this.model)},t.__name__=\"PanelHTMLBoxView\",t}(_.HTMLBoxView);i.PanelHTMLBoxView=u},\n \"12e90a1b7e\": function _(t,e,o){var i,n=this&&this.__extends||(i=function(t,e){return(i=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var o in e)e.hasOwnProperty(o)&&(t[o]=e[o])})(t,e)},function(t,e){function o(){this.constructor=t}i(t,e),t.prototype=null===e?Object.create(e):(o.prototype=e.prototype,new o)}),u=(this&&this.__importStar||function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var o in t)Object.hasOwnProperty.call(t,o)&&(e[o]=t[o]);return e.default=t,e})(t(\"@bokehjs/core/properties\")),l=t(\"@bokehjs/models/layouts/html_box\"),s=function(t){function e(){return null!==t&&t.apply(this,arguments)||this}return n(e,t),e.prototype.initialize=function(){t.prototype.initialize.call(this),this._blocked=!1,this._setting=!1,this._time=Date.now()},e.prototype.connect_signals=function(){var e=this;t.prototype.connect_signals.call(this),this.connect(this.model.properties.loop.change,function(){return e.set_loop()}),this.connect(this.model.properties.paused.change,function(){return e.set_paused()}),this.connect(this.model.properties.time.change,function(){return e.set_time()}),this.connect(this.model.properties.value.change,function(){return e.set_value()}),this.connect(this.model.properties.volume.change,function(){return e.set_volume()})},e.prototype.render=function(){var e=this;t.prototype.render.call(this),this.audioEl=document.createElement(\"audio\"),this.audioEl.controls=!0,this.audioEl.src=this.model.value,this.audioEl.currentTime=this.model.time,this.audioEl.loop=this.model.loop,null!=this.model.volume?this.audioEl.volume=this.model.volume/100:this.model.volume=100*this.audioEl.volume,this.audioEl.onpause=function(){return e.model.paused=!0},this.audioEl.onplay=function(){return e.model.paused=!1},this.audioEl.ontimeupdate=function(){return e.update_time(e)},this.audioEl.onvolumechange=function(){return e.update_volume(e)},this.el.appendChild(this.audioEl),this.model.paused||this.audioEl.play()},e.prototype.update_time=function(t){t._setting?t._setting=!1:Date.now()-t._time1&&\"number\"==typeof h[0]?l[u]=r.data[u].slice(c*h[1],c*h[1]+h[1]):l[u]=r.data[u][c]}a.push(l)}i.data=a}t&&this.updateDeck()},e.prototype._on_click_event=function(t){var e={coordinate:t.coordinate,lngLat:t.lngLat,index:t.index};this.model.clickState=e},e.prototype._on_hover_event=function(t){var e={coordinate:t.coordinate,lngLat:t.lngLat,index:t.index};this.model.hoverState=e},e.prototype._on_viewState_event=function(t){this.model.viewState=t.viewState},e.prototype.getData=function(){var t=this;return r(r({},this.model.data),{layers:this.model.layers,initialViewState:this.model.initialViewState,onViewStateChange:function(e){return t._on_viewState_event(e)},onClick:function(e){return t._on_click_event(e)},onHover:function(e){return t._on_hover_event(e)}})},e.prototype.updateDeck=function(){if(this.deckGL){var t=this.getData();if(d.updateDeck)d.updateDeck(t,this.deckGL);else{var e=this.jsonConverter.convert(t);this.deckGL.setProps(e)}}else this.render()},e.prototype.createDeck=function(t){var e,o=t.mapboxApiKey,n=t.container,i=t.jsonInput,a=t.tooltip;try{var s=this.jsonConverter.convert(i),c=u.makeTooltip(a);e=new d.DeckGL(r(r({},s),{map:f,mapboxApiAccessToken:o,container:n,getTooltip:c}))}catch(t){console.error(t)}return e},e.prototype.render=function(){t.prototype.render.call(this);var e=c.div({class:\"deckgl\"});_.set_size(e,this.model);var o=this.model.mapbox_api_key,n=this.model.tooltip,i=this.getData();d.createDeck?this.deckGL=d.createDeck({mapboxApiKey:o,container:e,jsonInput:i,tooltip:n}):this.deckGL=this.createDeck({mapboxApiKey:o,container:e,jsonInput:i,tooltip:n}),this.el.appendChild(e)},e.__name__=\"DeckGLPlotView\",e}(_.PanelHTMLBoxView);o.DeckGLPlotView=m;var k=function(t){function e(e){return t.call(this,e)||this}return i(e,t),e.init_DeckGLPlot=function(){this.prototype.default_view=m,this.define({data:[l.Any],data_sources:[l.Array,[]],clickState:[l.Any],hoverState:[l.Any],initialViewState:[l.Any],layers:[l.Array,[]],mapbox_api_key:[l.String],tooltip:[l.Any],viewState:[l.Any]}),this.override({height:400,width:600})},e.__name__=\"DeckGLPlot\",e.__module__=\"panel.models.deckgl\",e}(p.HTMLBox);o.DeckGLPlot=k,k.init_DeckGLPlot()},\n \"27d3545a25\": function _(e,t,n){var i,r,l={fontFamily:'\"Helvetica Neue\", Helvetica, Arial, sans-serif',display:\"flex\",flex:\"wrap\",maxWidth:\"500px\",flexDirection:\"column\",zIndex:2};function a(){return document.createElement(\"div\")}function o(e){if(!e.picked)return null;if(e.object===i)return r;var t={html:c(e.object),style:l};return r=t,i=e.object,t}n.getTooltipDefault=o;var s=new Set([\"position\",\"index\"]);function c(e){var t=a();for(var n in e)if(!s.has(n)){var i=a();i.className=\"header\",i.textContent=n;var r=a();r.className=\"value\",r.textContent=u(e[n]);var l=a();f(l,i,r),l.appendChild(i),l.appendChild(r),t.appendChild(l)}return t.innerHTML}function f(e,t,n){Object.assign(t.style,{fontWeight:700,marginRight:\"10px\",flex:\"1 1 0%\"}),Object.assign(n.style,{flex:\"none\",maxWidth:\"250px\",overflow:\"hidden\",whiteSpace:\"nowrap\",textOverflow:\"ellipsis\"}),Object.assign(e.style,{display:\"flex\",flexDirection:\"row\",justifyContent:\"space-between\",alignItems:\"stretch\"})}function u(e){var t;if(Array.isArray(e)&&e.length>4)t=\"Array<\"+e.length+\">\";else if(\"string\"==typeof e)t=e;else if(\"number\"==typeof e)t=String(e);else try{t=JSON.stringify(e)}catch(e){t=\"\"}return t.length>50&&(t=t.slice(0,50)),t}function p(e,t){var n=e;for(var i in t)n=n.replace(\"{\"+i+\"}\",t[i]);return n}n.tabularize=c,n.toText=u,n.substituteIn=p,n.makeTooltip=function(e){return e?e.html||e.text?function(t){if(!t.picked)return null;var n={style:e.style||l};return 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user-select:none;\",\"once\"==this.model.loop_policy?m.checked=!0:\"loop\"==this.model.loop_policy?f.checked=!0:y.checked=!0,this.loop_state.appendChild(m),this.loop_state.appendChild(_),this.loop_state.appendChild(f),this.loop_state.appendChild(v),this.loop_state.appendChild(y),this.loop_state.appendChild(x),this.el.appendChild(this.sliderEl),this.el.appendChild(i),this.el.appendChild(this.loop_state)},e.prototype.set_frame=function(t){this.model.value!=t&&(this.model.value=t),this.sliderEl.value!=String(t)&&(this.sliderEl.value=String(t))},e.prototype.get_loop_state=function(){for(var t=this.loop_state.state,e=0;e0?this.play_animation():this.model.direction<0&&this.reverse_animation()},e.prototype.faster=function(){this.model.interval=Math.round(.7*this.model.interval),this.model.direction>0?this.play_animation():this.model.direction<0&&this.reverse_animation()},e.prototype.anim_step_forward=function(){if(this.model.valuethis.model.start)this.previous_frame();else{var t=this.get_loop_state();\"loop\"==t?this.last_frame():\"reflect\"==t?(this.first_frame(),this.play_animation()):(this.pause_animation(),this.first_frame())}},e.prototype.pause_animation=function(){this.model.direction=0,this.timer&&(clearInterval(this.timer),this.timer=null)},e.prototype.play_animation=function(){var t=this;this.pause_animation(),this.model.direction=1,this.timer||(this.timer=setInterval(function(){return t.anim_step_forward()},this.model.interval))},e.prototype.reverse_animation=function(){var t=this;this.pause_animation(),this.model.direction=-1,this.timer||(this.timer=setInterval(function(){return t.anim_step_reverse()},this.model.interval))},e.__name__=\"PlayerView\",e}(a.WidgetView);i.PlayerView=l;var d=function(t){function e(e){return t.call(this,e)||this}return o(e,t),e.init_Player=function(){this.prototype.default_view=l,this.define({direction:[r.Number,0],interval:[r.Number,500],start:[r.Number],end:[r.Number],step:[r.Number,1],loop_policy:[r.Any,\"once\"],value:[r.Any,0]}),this.override({width:400})},e.__name__=\"Player\",e.__module__=\"panel.models.widgets\",e}(a.Widget);i.Player=d,d.init_Player()},\n \"d46f026c83\": function _(t,e,o){var r,n=this&&this.__extends||(r=function(t,e){return(r=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var o in e)e.hasOwnProperty(o)&&(t[o]=e[o])})(t,e)},function(t,e){function o(){this.constructor=t}r(t,e),t.prototype=null===e?Object.create(e):(o.prototype=e.prototype,new o)}),i=(this&&this.__importStar||function(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var o in t)Object.hasOwnProperty.call(t,o)&&(e[o]=t[o]);return e.default=t,e})(t(\"@bokehjs/core/properties\")),l=t(\"@bokehjs/core/util/object\"),a=t(\"@bokehjs/core/util/eq\"),p=t(\"@bokehjs/models/layouts/html_box\"),s=t(\"99a25e6992\"),u=t(\"62ba79515f\"),c=t(\"ec60963462\"),_=window.Plotly,d=function(t,e,o){var r=Array.isArray(e)?[]:{};if(\"click\"===o||\"hover\"===o||\"selected\"===o){var n=[];if(null==e)return null;for(var i=t.data,l=0;l1){for(var u=[],c=0;c=0?t=setTimeout(i,l-c):(t=null,u||(r=n.apply(o,e),o=e=null))}null==l&&(l=100);var c=function(){o=this,e=arguments,a=Date.now();var c=u&&!t;return t||(t=setTimeout(i,l)),c&&(r=n.apply(o,e),o=e=null),r};return c.clear=function(){t&&(clearTimeout(t),t=null)},c.flush=function(){t&&(r=n.apply(o,e),o=e=null,clearTimeout(t),t=null)},c}t.debounce=t,l.exports=t},\n \"62ba79515f\": function _(t,r,n){n.get=function(t,r,n){void 0===n&&(n=void 0);var e=function(n){return String.prototype.split.call(r,n).filter(Boolean).reduce(function(t,r){return null!=t?t[r]:t},t)},o=e(/[,[\\]]+?/)||e(/[,[\\].]+?/);return void 0===o||o===t?n:o},n.throttle=function(t,r){var n=0;return function(){var e=Number(new Date);e-n>=r&&(t(),n=e)}},n.deepCopy=function t(r){var n;if(null==r||\"object\"!=typeof r)return r;if(r instanceof Array){n=[];for(var e=0,o=r.length;e0){var t=this._fetch_datasets();if(\"data\"in t&&(this.model.data.data.values=t.data,delete t.data),void 0!==this.model.data.data)for(var e=0,o=this.model.data.data;e0&&(this.timer=setInterval(function(){return t.snapshot()},this.model.timeout))},e.prototype.snapshot=function(){this.canvasEl.width=this.videoEl.videoWidth,this.canvasEl.height=this.videoEl.videoHeight;var t=this.canvasEl.getContext(\"2d\");t&&t.drawImage(this.videoEl,0,0,this.canvasEl.width,this.canvasEl.height),this.model.value=this.canvasEl.toDataURL(\"image/\"+this.model.format,.95)},e.prototype.remove=function(){t.prototype.remove.call(this),this.timer&&(clearInterval(this.timer),this.timer=null)},e.prototype.render=function(){var e=this;t.prototype.render.call(this),this.videoEl||(this.videoEl=document.createElement(\"video\"),this.model.sizing_mode&&\"fixed\"!==this.model.sizing_mode||(this.model.height&&(this.videoEl.height=this.model.height),this.model.width&&(this.videoEl.width=this.model.width)),this.videoEl.style.objectFit=\"fill\",this.videoEl.style.minWidth=\"100%\",this.videoEl.style.minHeight=\"100%\",this.canvasEl=document.createElement(\"canvas\"),this.el.appendChild(this.videoEl),navigator.mediaDevices.getUserMedia&&navigator.mediaDevices.getUserMedia(this.constraints).then(function(t){e.videoEl.srcObject=t,e.model.paused||e.videoEl.play()}).catch(console.error))},e.__name__=\"VideoStreamView\",e}(t(\"ec60963462\").PanelHTMLBoxView);i.VideoStreamView=h;var a=function(t){function e(e){return t.call(this,e)||this}return n(e,t),e.init_VideoStream=function(){this.prototype.default_view=h,this.define({format:[s.String,\"png\"],paused:[s.Boolean,!1],snapshot:[s.Boolean,!1],timeout:[s.Number,0],value:[s.Any]}),this.override({height:240,width:320})},e.__name__=\"VideoStream\",e.__module__=\"panel.models.widgets\",e}(r.HTMLBox);i.VideoStream=a,a.init_VideoStream()},\n \"63070bc9ce\": function _(V,o,e){var l=V(\"1a4b530306\");e.VTKPlot=l.VTKPlot;var K=V(\"b933e81f56\");e.VTKVolumePlot=K.VTKVolumePlot;var T=V(\"5bc27423fe\");e.VTKAxes=T.VTKAxes},\n \"1a4b530306\": function _(e,t,n){var i,o=this&&this.__extends||(i=function(e,t){return(i=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(e,t){e.__proto__=t}||function(e,t){for(var n in t)t.hasOwnProperty(n)&&(e[n]=t[n])})(e,t)},function(e,t){function n(){this.constructor=e}i(e,t),e.prototype=null===t?Object.create(t):(n.prototype=t.prototype,new n)}),r=(this&&this.__importStar||function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t})(e(\"@bokehjs/core/properties\")),a=e(\"@bokehjs/core/dom\"),s=e(\"7620c2cc05\"),c=e(\"3b847a648d\"),d=function(e){function t(){var t=null!==e&&e.apply(this,arguments)||this;return t._axes_initialized=!1,t}return o(t,e),t.prototype.connect_signals=function(){var t=this;e.prototype.connect_signals.call(this),this.connect(this.model.properties.axes.change,function(){t._delete_axes(),t.model.axes&&t._set_axes(),t._vtk_renwin.getRenderWindow().render()}),this.el.addEventListener(\"mouseenter\",function(){var e=t._vtk_renwin.getInteractor();t.model.enable_keybindings&&(document.querySelector(\"body\").addEventListener(\"keypress\",e.handleKeyPress),document.querySelector(\"body\").addEventListener(\"keydown\",e.handleKeyDown),document.querySelector(\"body\").addEventListener(\"keyup\",e.handleKeyUp))}),this.el.addEventListener(\"mouseleave\",function(){var e=t._vtk_renwin.getInteractor();document.querySelector(\"body\").removeEventListener(\"keypress\",e.handleKeyPress),document.querySelector(\"body\").removeEventListener(\"keydown\",e.handleKeyDown),document.querySelector(\"body\").removeEventListener(\"keyup\",e.handleKeyUp)})},t.prototype.render=function(){e.prototype.render.call(this),this._axes=null,this._axes_initialized=!1,this._plot()},t.prototype.after_layout=function(){this._axes_initialized||(this._render_axes_canvas(),this._axes_initialized=!0)},t.prototype._render_axes_canvas=function(){var e=this,t=this._vtk_container.getElementsByTagName(\"canvas\");if(1!=t.length)throw Error(\"Error at initialization of the 3D scene, container should have one and only one canvas\");t[0].classList.add(\"scene3d-canvas\");var n=a.canvas({style:{position:\"absolute\",top:\"0\",left:\"0\",width:\"100%\",height:\"100%\"}});n.classList.add(\"axes-canvas\"),this._vtk_container.appendChild(n),this._vtk_renwin.setResizeCallback(function(){var t=e._vtk_container.getBoundingClientRect(),i=Math.floor(t.width*window.devicePixelRatio),o=Math.floor(t.height*window.devicePixelRatio);n.setAttribute(\"width\",i.toFixed()),n.setAttribute(\"height\",o.toFixed())})},t.prototype._delete_axes=function(){var e=this;if(null!=this._axes){Object.keys(this._axes).forEach(function(t){return e._vtk_renwin.getRenderer().removeActor(e._axes[t])});var t=this._vtk_renwin.getContainer().getElementsByClassName(\"axes-canvas\")[0],n=t.getContext(\"2d\");n&&n.clearRect(0,0,t.clientWidth*window.devicePixelRatio,t.clientHeight*window.devicePixelRatio),this._axes=null}},t.prototype._set_axes=function(){if(this.model.axes){var e=this._vtk_renwin.getContainer().getElementsByClassName(\"axes-canvas\")[0],t=this.model.axes.create_axes(e),n=t.psActor,i=t.axesActor,o=t.gridActor;this._axes={psActor:n,axesActor:i,gridActor:o},this._vtk_renwin.getRenderer().addActor(n),this._vtk_renwin.getRenderer().addActor(i),this._vtk_renwin.getRenderer().addActor(o)}},t.prototype._plot=function(){var e=this;if(this.model.data)var t=c.vtkns.DataAccessHelper.get(\"zip\",{zipContent:atob(this.model.data),callback:function(n){var i=c.vtkns.HttpSceneLoader.newInstance({renderer:e._vtk_renwin.getRenderer(),dataAccessHelper:t}),o=c.vtk.macro.debounce(function(){null==e._axes&&e.model.axes&&e._set_axes(),e.model.properties.camera.change.emit()},100);i.setUrl(\"index.json\"),i.onReady(o)}});else this._vtk_renwin.getRenderWindow().render()},t.__name__=\"VTKPlotView\",t}(s.AbstractVTKView);n.VTKPlotView=d;var l=function(e){function t(t){var n=e.call(this,t)||this;n.outline=c.vtkns.OutlineFilter.newInstance();var i=c.vtkns.Mapper.newInstance();return i.setInputConnection(n.outline.getOutputPort()),n.outline_actor=c.vtkns.Actor.newInstance(),n.outline_actor.setMapper(i),n}return o(t,e),t.init_VTKPlot=function(){this.prototype.default_view=d,this.define({data:[r.String],axes:[r.Instance],enable_keybindings:[r.Boolean,!1]})},t.__name__=\"VTKPlot\",t}(s.AbstractVTKPlot);n.VTKPlot=l,l.init_VTKPlot()},\n \"7620c2cc05\": function _(e,t,n){var i,r=this&&this.__extends||(i=function(e,t){return(i=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(e,t){e.__proto__=t}||function(e,t){for(var n in t)t.hasOwnProperty(n)&&(e[n]=t[n])})(e,t)},function(e,t){function n(){this.constructor=e}i(e,t),e.prototype=null===t?Object.create(t):(n.prototype=t.prototype,new n)}),o=(this&&this.__importStar||function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t})(e(\"@bokehjs/core/properties\")),a=e(\"@bokehjs/core/dom\"),s=e(\"@bokehjs/core/util/object\"),_=e(\"@bokehjs/models/layouts/html_box\"),c=e(\"ec60963462\"),d=e(\"3b847a648d\"),h=function(e){function t(){var t=null!==e&&e.apply(this,arguments)||this;return t._setting_camera=!1,t}return r(t,e),t.prototype.connect_signals=function(){var t=this;e.prototype.connect_signals.call(this),this.connect(this.model.properties.data.change,function(){t.invalidate_render()}),this.connect(this.model.properties.orientation_widget.change,function(){t._orientation_widget_visibility(t.model.orientation_widget)}),this.connect(this.model.properties.camera.change,function(){return t._set_camera_state()})},t.prototype._orientation_widget_visibility=function(e){this._orientationWidget.setEnabled(e),e?this._widgetManager.enablePicking():this._widgetManager.disablePicking(),this._orientationWidget.updateMarkerOrientation(),this._vtk_renwin.getRenderWindow().render()},t.prototype._create_orientation_widget=function(){var e=this,t=d.vtkns.AxesActor.newInstance(),n=d.vtkns.OrientationMarkerWidget.newInstance({actor:t,interactor:this._vtk_renwin.getInteractor()});n.setEnabled(!0),n.setViewportCorner(d.vtkns.OrientationMarkerWidget.Corners.BOTTOM_RIGHT),n.setViewportSize(.15),n.setMinPixelSize(100),n.setMaxPixelSize(300),this._orientationWidget=n;var i=d.vtkns.WidgetManager.newInstance();i.setRenderer(n.getRenderer());var r=d.vtkns.InteractiveOrientationWidget.newInstance();r.placeWidget(t.getBounds()),r.setBounds(t.getBounds()),r.setPlaceFactor(1);var o=i.addWidget(r);this._widgetManager=i,o.onOrientationChange(function(t){var n=t.direction,i=e._vtk_renwin.getRenderer().getActiveCamera(),r=i.getFocalPoint(),o=i.getPosition(),a=i.getViewUp(),s=Math.sqrt(Math.pow(o[0]-r[0],2)+Math.pow(o[1]-r[1],2)+Math.pow(o[2]-r[2],2));i.setPosition(r[0]+n[0]*s,r[1]+n[1]*s,r[2]+n[2]*s),n[0]&&i.setViewUp(d.majorAxis(a,1,2)),n[1]&&i.setViewUp(d.majorAxis(a,0,2)),n[2]&&i.setViewUp(d.majorAxis(a,0,1)),e._orientationWidget.updateMarkerOrientation(),e._vtk_renwin.getRenderer().resetCameraClippingRange(),e._vtk_renwin.getRenderWindow().render()}),this._orientation_widget_visibility(this.model.orientation_widget)},t.prototype._get_camera_state=function(){if(!this._setting_camera){this._setting_camera=!0;var e=s.clone(this._vtk_renwin.getRenderer().getActiveCamera().get());delete e.classHierarchy,delete e.vtkObject,delete e.vtkCamera,delete e.viewPlaneNormal,this.model.camera=e,this._setting_camera=!1}},t.prototype._set_camera_state=function(){if(!this._setting_camera){this._setting_camera=!0;try{this.model.camera&&this._vtk_renwin.getRenderer().getActiveCamera().set(this.model.camera)}finally{this._setting_camera=!1}this._orientationWidget.updateMarkerOrientation(),this._vtk_renwin.getRenderer().resetCameraClippingRange(),this._vtk_renwin.getRenderWindow().render()}},t.prototype.render=function(){var t=this;e.prototype.render.call(this),this._orientationWidget=null,this._vtk_container=a.div(),c.set_size(this._vtk_container,this.model),this.el.appendChild(this._vtk_container),this._vtk_renwin=d.vtkns.FullScreenRenderWindow.newInstance({rootContainer:this.el,container:this._vtk_container}),this._remove_default_key_binding(),this._create_orientation_widget(),this._vtk_renwin.getRenderer().getActiveCamera().onModified(function(){return t._get_camera_state()}),this._set_camera_state(),this.model.renderer_el=this._vtk_renwin},t.prototype.after_layout=function(){e.prototype.after_layout.call(this),this._vtk_renwin.resize()},t.prototype._remove_default_key_binding=function(){var e=this._vtk_renwin.getInteractor();document.querySelector(\"body\").removeEventListener(\"keypress\",e.handleKeyPress),document.querySelector(\"body\").removeEventListener(\"keydown\",e.handleKeyDown),document.querySelector(\"body\").removeEventListener(\"keyup\",e.handleKeyUp)},t.__name__=\"AbstractVTKView\",t}(c.PanelHTMLBoxView);n.AbstractVTKView=h;var l=function(e){function t(t){return e.call(this,t)||this}return r(t,e),t.prototype.getActors=function(){return this.renderer_el.getRenderer().getActors()},t.init_AbstractVTKPlot=function(){this.define({orientation_widget:[o.Boolean,!1],camera:[o.Instance]}),this.override({height:300,width:300})},t.__name__=\"AbstractVTKPlot\",t.__module__=\"panel.models.vtk\",t}(_.HTMLBox);n.AbstractVTKPlot=l,l.init_AbstractVTKPlot()},\n \"3b847a648d\": function _(e,t,n){var r=e(\"@bokehjs/core/util/serialization\"),a=e(\"@bokehjs/core/util/array\");function o(e){var t=Math.min(Math.max(Math.round(e),0),255).toString(16);return 2==t.length?t:\"0\"+t}function i(e,t,n){return\"#\"+o(e)+o(t)+o(n)}function v(e){for(var t=new ArrayBuffer(e.length),n=new Uint8Array(t),r=0,a=e.length;rMath.abs(e[n])?t:n,o=e[a]>0?1:-1;return r[a]=o,r},n.cartesian_product=function(){for(var e=[],t=0;t=.005&&(e.model.sampling=t)}),Math.abs(this.model.sampling-Number(this.shadow_selector.value))>=.005&&this.model.properties.sampling.change.emit(),this.edge_gradient_slider.addEventListener(\"input\",function(){var t=Number(e.edge_gradient_slider.value);Math.abs(e.model.edge_gradient-t)>=.005&&(e.model.edge_gradient=t)}),Math.abs(this.model.edge_gradient-Number(this.edge_gradient_slider.value))>=.005&&this.model.properties.edge_gradient.change.emit()},t.prototype._plot_volume=function(){var e=this,t=this._vtk_image_data,n=a.vtkns.Volume.newInstance(),r=a.vtkns.VolumeMapper.newInstance();n.setMapper(r),r.setInputData(t);var i=(t.getPointData().getScalars()||t.getPointData().getArrays()[0]).getRange(),o=a.vtkns.ColorTransferFunction.newInstance();o.onModified(function(){return e.model.mapper=a.vtkLutToMapper(o)});var s=a.vtkns.PiecewiseFunction.newInstance(),l=.7*Math.sqrt(t.getSpacing().map(function(e){return e*e}).reduce(function(e,t){return e+t},0));r.setSampleDistance(l),n.getProperty().setRGBTransferFunction(0,o),n.getProperty().setScalarOpacity(0,s),n.getProperty().setInterpolationTypeToFastLinear(),n.getProperty().setScalarOpacityUnitDistance(0,a.vtkns.BoundingBox.getDiagonalLength(t.getBounds())/Math.max.apply(Math,t.getDimensions())),n.getProperty().setGradientOpacityMinimumValue(0,0),n.getProperty().setGradientOpacityMaximumValue(0,.05*(i[1]-i[0])),n.getProperty().setShade(this.model.shadow),n.getProperty().setUseGradientOpacity(0,!0),n.getProperty().setGradientOpacityMinimumOpacity(0,0),n.getProperty().setGradientOpacityMaximumOpacity(0,1),n.getProperty().setAmbient(this.model.ambient),n.getProperty().setDiffuse(this.model.diffuse),n.getProperty().setSpecular(this.model.specular),n.getProperty().setSpecularPower(this.model.specular_power),this._vtk_renwin.getRenderer().addVolume(n),this._controllerWidget.setupContent(this._vtk_renwin.getRenderWindow(),n,!0)},t.prototype._plot_slices=function(){var e=this._vtk_image_data,t=a.vtkns.ImageSlice.newInstance(),n=a.vtkns.ImageSlice.newInstance(),r=a.vtkns.ImageSlice.newInstance(),i=a.vtkns.ImageMapper.newInstance(),o=a.vtkns.ImageMapper.newInstance(),s=a.vtkns.ImageMapper.newInstance();i.setInputData(e),i.setISlice(this.model.slice_i),t.setMapper(i),o.setInputData(e),o.setJSlice(this.model.slice_j),n.setMapper(o),s.setInputData(e),s.setKSlice(this.model.slice_k),r.setMapper(s);var l=a.vtkns.PiecewiseFunction.newInstance();l.removeAllPoints(),l.addPoint(0,1);var c=this.volume.getProperty().getRGBTransferFunction(0),p=t.getProperty();n.setProperty(p),r.setProperty(p),p.setRGBTransferFunction(c),p.setScalarOpacity(l);var d=this._vtk_renwin.getRenderer();d.addActor(t),d.addActor(n),d.addActor(r)},t.prototype._set_volume_visibility=function(e){this.volume.setVisibility(e)},t.prototype._set_slices_visibility=function(e){this._vtk_renwin.getRenderer().getActors().map(function(t){return t.setVisibility(e)})},t.__name__=\"VTKVolumePlotView\",t}(s.AbstractVTKView);n.VTKVolumePlotView=l;var c=function(e){function t(t){return e.call(this,t)||this}return i(t,e),t.init_VTKVolumePlot=function(){this.prototype.default_view=l,this.define({data:[o.Instance],shadow:[o.Boolean,!0],sampling:[o.Number,.4],edge_gradient:[o.Number,.2],colormap:[o.String],rescale:[o.Boolean,!1],ambient:[o.Number,.2],diffuse:[o.Number,.7],specular:[o.Number,.3],specular_power:[o.Number,8],slice_i:[o.Int,0],slice_j:[o.Int,0],slice_k:[o.Int,0],display_volume:[o.Boolean,!0],display_slices:[o.Boolean,!1],render_background:[o.String,\"#52576e\"],interpolation:[o.Any,\"fast_linear\"],mapper:[o.Instance]})},t.__name__=\"VTKVolumePlot\",t}(s.AbstractVTKPlot);n.VTKVolumePlot=c,c.init_VTKVolumePlot()},\n \"5bc27423fe\": function _(t,e,i){var s,n=this&&this.__extends||(s=function(t,e){return(s=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var i in 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t[0]=(1-(l+m))*S,t[1]=(c+P)*S,t[2]=(b-y)*S,t[3]=0,t[4]=(c-P)*O,t[5]=(1-(f+m))*O,t[6]=(v+p)*O,t[7]=0,t[8]=(b+y)*E,t[9]=(v-p)*E,t[10]=(1-(f+l))*E,t[11]=0,t[12]=n[0],t[13]=n[1],t[14]=n[2],t[15]=1,t},n.fromRotationTranslationScaleOrigin=function(t,a,n,r,o){var e=a[0],u=a[1],h=a[2],i=a[3],M=e+e,s=u+u,f=h+h,c=e*M,b=e*s,l=e*f,v=u*s,m=u*f,p=h*f,y=i*M,P=i*s,S=i*f,O=r[0],E=r[1],I=r[2],L=o[0],N=o[1],R=o[2],x=(1-(v+p))*O,d=(b+S)*O,g=(l-P)*O,A=(b-S)*E,Y=(1-(c+p))*E,T=(m+y)*E,w=(l+P)*I,_=(m-y)*I,q=(1-(c+v))*I;return t[0]=x,t[1]=d,t[2]=g,t[3]=0,t[4]=A,t[5]=Y,t[6]=T,t[7]=0,t[8]=w,t[9]=_,t[10]=q,t[11]=0,t[12]=n[0]+L-(x*L+A*N+w*R),t[13]=n[1]+N-(d*L+Y*N+_*R),t[14]=n[2]+R-(g*L+T*N+q*R),t[15]=1,t},n.fromQuat=function(t,a){var n=a[0],r=a[1],o=a[2],e=a[3],u=n+n,h=r+r,i=o+o,M=n*u,s=r*u,f=r*h,c=o*u,b=o*h,l=o*i,v=e*u,m=e*h,p=e*i;return t[0]=1-f-l,t[1]=s+p,t[2]=c-m,t[3]=0,t[4]=s-p,t[5]=1-M-l,t[6]=b+v,t[7]=0,t[8]=c+m,t[9]=b-v,t[10]=1-M-f,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,t},n.frustum=function(t,a,n,r,o,e,u){var h=1/(n-a),i=1/(o-r),M=1/(e-u);return t[0]=2*e*h,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=2*e*i,t[6]=0,t[7]=0,t[8]=(n+a)*h,t[9]=(o+r)*i,t[10]=(u+e)*M,t[11]=-1,t[12]=0,t[13]=0,t[14]=u*e*2*M,t[15]=0,t},n.perspective=function(t,a,n,r,o){var e,u=1/Math.tan(a/2);t[0]=u/n,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=u,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[11]=-1,t[12]=0,t[13]=0,t[15]=0,null!=o&&o!==1/0?(e=1/(r-o),t[10]=(o+r)*e,t[14]=2*o*r*e):(t[10]=-1,t[14]=-2*r);return t},n.perspectiveFromFieldOfView=function(t,a,n,r){var o=Math.tan(a.upDegrees*Math.PI/180),e=Math.tan(a.downDegrees*Math.PI/180),u=Math.tan(a.leftDegrees*Math.PI/180),h=Math.tan(a.rightDegrees*Math.PI/180),i=2/(u+h),M=2/(o+e);return 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sigma\n", - "\n", - " ###### Bokeh Figures #######\n", - "\n", - "def peak_fig(signal, hist, edges, peak_idx, left, right):\n", - " \"\"\"General histogram plotter with peak location and left/right limits plotted\"\"\"\n", - " low = round(edges[left], 2)\n", - " hi = round(edges[right], 2)\n", - " fig = figure(\n", - " title='Used Intensity Distribution for {0}. Low/Hi: {1}/{2}'.format(signal, low, hi),\n", - " x_axis_label='Intensity Values',\n", - " y_axis_label='Counts'\n", - " )\n", - " fig.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:])\n", - " left_line = Span(location=edges[left], dimension='height', line_color='black')\n", - " right_line = Span(location=edges[right], dimension='height', line_color='black')\n", - " peak_line = Span(location=edges[peak_idx], dimension='height', line_color='red')\n", - " fig.renderers.extend([left_line, right_line, peak_line])\n", - "\n", - " return fig\n", - "\n", - "def azav_fig(ave_azav, peak, intensity, delta_bin):\n", - " \"\"\"Generate the azav fig for html file\"\"\"\n", - " x_vals = np.arange(len(ave_azav))\n", - " fig = figure(\n", - " title='Average Azimuthal Binned Array: Center - {0}, min/max - {1}/{2}, intensity - {3}'.format(peak, peak-delta_bin, peak+delta_bin, round(intensity, 2)),\n", - " x_axis_label='Bins',\n", - " y_axis_label='Intensity',\n", - " )\n", - "\n", - " peak_line = Span(location=peak, dimension='height', line_color='green', line_width=2)\n", - " lower_line = Span(location=peak-delta_bin, dimension='height', line_color='black')\n", - " upper_line = Span(location=peak+delta_bin, dimension='height', line_color='black')\n", - " ave_azav_curve = fig.scatter(x_vals, ave_azav)\n", - " fig.renderers.extend([peak_line, lower_line, upper_line])\n", - "\n", - " azav_legend = Legend(items=[\n", - " LegendItem(label='Azimuthal Average', renderers=[ave_azav_curve])\n", - " ])\n", - " fig.add_layout(azav_legend)\n", - "\n", - " return fig\n", - "\n", - "def intensity_hist(intensity_hist, edges):\n", - " fig = figure(\n", - " title='Intensity Histogram'\n", - " )\n", - " fig.quad(top=intensity_hist, bottom=0, left=edges[:-1], right=edges[1:])\n", - "\n", - " return fig\n", - "\n", - "def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma):\n", - " \"\"\"Simple plot of intensity vs peak value\"\"\"\n", - " fig = figure(\n", - " title='Peak value vs Intensity. Slope = {0}, Intercept = {1}'.format(round(slope, 2), round(intercept, 2)),\n", - " x_axis_label='Intensity Monitor Value',\n", - " y_axis_label='Peak Values'\n", - " )\n", - " fig.x_range.range_padding = fig.y_range.range_padding = 0\n", - " h, y_edge, x_edge = np.histogram2d(peak_vals, intensity, bins=100)\n", - " fig.image(image=[h], x=x_edge[0], y=y_edge[0], dh=y_edge[-1]-y_edge[0], dw=x_edge[-1]-x_edge[0], palette=\"Spectral11\")\n", - " color_mapper = LinearColorMapper(palette=\"Spectral11\", low=h.min(), high=h.max())\n", - " color_bar = ColorBar(color_mapper=color_mapper, location=(0,0))\n", - " fig.xaxis.bounds = [i0_low, i0_high]\n", - " fig.add_layout(color_bar, 'right')\n", - " fig.line(x, y, color='red')\n", - " fig.line(x, y - 1 * sigma, color='orange')\n", - " fig.line(x, y + 1 * sigma, color='orange')\n", - " return fig" - ] - }, - { - "cell_type": "code", - "execution_count": 45, - "metadata": { - "scrolled": true - }, - "outputs": [], - "source": [ - "# Find I0 distribution and filter out unused values\n", - "i0_data = np.array(i0_data)\n", - "i0_hist, i0_edges, i0_peak_idx, i0_left_idx, i0_right_idx = peak_lr(i0_data)\n", - "i0_low = i0_edges[i0_left_idx]\n", - "i0_high = i0_edges[i0_right_idx]\n", - "i0_idxs = np.where((i0_data > i0_low) & (i0_data < i0_high))\n", - "i0_data_use = i0_data[i0_idxs]\n", - "\n", - "# Filter on I0 data to get points we will evaluate\n", - "hist_peak, edges_peak, peak_idx, left_peak, right_peak = peak_lr(i0_data_use)\n", - "p = peak_fig('gdet', hist_peak, edges_peak, peak_idx, left_peak, right_peak)\n", - "\n", - "# Get the azav value we'll use\n", - "azav_use = [azav_data[idx] for idx in i0_idxs[0]]\n", - "ave_azav = np.array((np.sum(azav_use, axis=0)) / len(azav_use))\n", - "# Find the peak bin from average azav values\n", - "peak = calc_azav_peak(ave_azav)\n", - "peak=25\n", - "\n", - "# Get the integrated intensity and generate fig\n", - "integrated_intensity = get_integrated_intensity(ave_azav, peak, DELTA_BIN)\n", - "p1 = azav_fig(ave_azav, peak, integrated_intensity, DELTA_BIN)\n", - "\n", - "\n", - "# Go back through indices and find peak values for all the intensities\n", - "low = peak - DELTA_BIN\n", - "high = peak + DELTA_BIN\n", - "peak_vals = [azav[low:high].sum(axis=0) for azav in azav_use]\n", - "# Now fit I0 vs diffraction intensities\n", - "x, y, slope, intercept, sigma = fit_limits(i0_data_use, peak_vals, i0_low, i0_high)\n", - "p2 = intensity_vs_peak_fig(i0_data_use, peak_vals, x, y, slope, intercept, sigma)\n" - ] - }, - { - "cell_type": "code", - "execution_count": 46, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "
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- "show(p)\n", - "show(p1)\n", - "show(p2)" - ] - }, - { - "cell_type": "code", - "execution_count": 56, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{'low_intercept': -3630.119742500365, 'ave_peak_intensity': 6332.59, 'delta_bin': 5, 'high_i0': 0.8466769609192851, 'ave_i0': 0.6414089038877722, 'peak_bin': 25, 'low_slope': 15036.018845158875, 'low_i0': 0.41789974458224605}\n" - ] - } - ], - "source": [ - "results = {\n", - " 'low_slope': slope,\n", - " 'low_intercept': intercept,\n", - " 'low_i0': i0_low,\n", - " 'high_i0': i0_high,\n", - " 'ave_i0': i0_data.mean(),\n", - " 'ave_peak_intensity': integrated_intensity,\n", - " 'peak_bin': peak,\n", - " 'delta_bin': DELTA_BIN\n", - "}\n", - "\n", - "\n", - "#After processing\n", - "# Peak bin\n", - "# low and hi delta_r around peak bin\n", - "# Io low bound and high bound\n", - "# Average Io\n", - "# Average integrated intensity\n", - "# slope and intercept of fit of 2D plot\n", - "# sigma around line fit\n", - "# Run number\n", - "\n", - "print(results)" - ] - }, - { - "cell_type": "code", - "execution_count": 54, - "metadata": {}, - "outputs": [ - { - "ename": "OSError", - "evalue": "[Errno 13] Permission denied: '/cds/home/opr/cxiopr/experiments/cxilv9518/jt_cal'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m\u001b[0m", - "\u001b[0;31mOSError\u001b[0mTraceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0mpath\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'/cds/home/opr/cxiopr/experiments/cxilv9518/jt_cal/run148/'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 6\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0misdir\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 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max_height=1000)\n", - "gspec[0:3, 0:3] = p\n", - "gspec[4:6, 0:3] = p1\n", - "gspec[7:9, 0:3] = p2\n", - "path = '/cds/home/opr/cxiopr/experiments/cxilv9518/jt_cal/run148/'\n", - "if not os.path.isdir(path):\n", - " os.makedirs(path)\n", - "gspec.save(''.join([path, 'report.html']))" - ] - }, - { - "cell_type": "code", - "execution_count": 51, - "metadata": {}, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "LCLS-I py2", - "language": "python", - "name": "ana1-current" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 2 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.15" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} From 6d4d6be7d46d0393e44b5a0f56a2dbdcf95c5bad Mon Sep 17 00:00:00 2001 From: Adam Date: Wed, 10 Mar 2021 15:35:35 -0800 Subject: [PATCH 09/23] MNT: Remove unused config file --- .../mpi_configs/smalldata_plot.yml | 71 ------------------- 1 file changed, 71 deletions(-) delete mode 100644 jet_tracking/mpi_scripts/mpi_configs/smalldata_plot.yml diff --git a/jet_tracking/mpi_scripts/mpi_configs/smalldata_plot.yml b/jet_tracking/mpi_scripts/mpi_configs/smalldata_plot.yml deleted file mode 100644 index 8bc2555..0000000 --- a/jet_tracking/mpi_scripts/mpi_configs/smalldata_plot.yml +++ /dev/null @@ -1,71 +0,0 @@ -master: - server: daq-cxi-mon05 - port: 5000 - -ipm_ttampl: - port: 5014 - var1: ipm2__sum - var2: tt__AMPL - number_of_events: 1200 - width: 900 - height: 600 - updateRate: 2 - xRange: - - auto - - 0.4 - yRange: - - auto - - 2000. - -ipm_ROI: - port: 5015 - var1: ipm2__sum - var2: jungfrau512k__ROI_1 - number_of_events: 1200 - width: 900 - height: 600 - updateRate: 2 - xRange: - - auto - - 0.4 - yRange: - - auto - - 2000. - -ROI_scan: - port: 5016 - i0var: ipm2__sum - sigvar: jungfrau512k__ROI_1 - binWidth: 100 - binEntries: 50 - FilterVar: - - lightStatus__xray - - ipm2__sum - FilterVarMin: - - 0.5 - - 50 - FilterVarMax: - - 1.5 - - 1000000. - width: 900 - height: 600 - updateRate: 2 - xRange: - - auto - - 0.4 - yRange: - - auto - - 2000. - -tt_fltpos_time: - port: 5015 - var1: ttall - var1_idx: 0 - number_of_events: 14400 - width: 900 - height: 300 - updateRate: 5 - yRange: - - auto - - 2000. - From 88143c7b7a83bf81560d92482e9ed89d75810515 Mon Sep 17 00:00:00 2001 From: Adam Date: Sat, 13 Mar 2021 16:57:50 -0800 Subject: [PATCH 10/23] new config file --- jet_tracking/jet_tracking_cal/jt_cal.py | 9 ++++---- .../{default_config.yml => cxi_config.yml} | 0 .../mpi_scripts/mpi_configs/xcs_config.yml | 23 +++++++++++++++++++ 3 files changed, 28 insertions(+), 4 deletions(-) rename jet_tracking/mpi_scripts/mpi_configs/{default_config.yml => cxi_config.yml} (100%) create mode 100644 jet_tracking/mpi_scripts/mpi_configs/xcs_config.yml diff --git a/jet_tracking/jet_tracking_cal/jt_cal.py b/jet_tracking/jet_tracking_cal/jt_cal.py index 1e1d6ca..42cb5cb 100644 --- a/jet_tracking/jet_tracking_cal/jt_cal.py +++ b/jet_tracking/jet_tracking_cal/jt_cal.py @@ -21,7 +21,7 @@ # Constants # Location of my branch for testing -JT_LOC = '/cds/home/a/aegger/jet_tracking/jet_tracking/' +JT_LOC = '/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/' # Number of bins BINS = 100 # Number of events to process @@ -331,7 +331,7 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): parser.add_argument('--run', type=str, \ default=(os.environ.get('RUN_NUM', None))) parser.add_argument('--cfg', type=str, \ - default=(''.join([JT_LOC, 'mpi_scripts/mpi_configs/default_config.yml']))) + default=(''.join([JT_LOC, 'mpi_scripts/mpi_configs/xcs_config.yml']))) parser.add_argument('--delta_bin', type=int, \ default=(DELTA_BIN)) parser.add_argument('--bins', type=int, \ @@ -362,7 +362,7 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): masks = get_r_masks(det_map['shape'], args.bins) i0_data = [] azav_data=[] - ped = detector.pedestals(1)[0] + ped = detector.pedestals(int(args.run))[0] logger.info('starting to evaluate 1000 events') for evt_idx, evt in enumerate(ds.events()): @@ -374,7 +374,8 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): azav = np.array([np.mean(image[mask]) for mask in masks]) azav_data.append(azav) try: - i0_data.append(ipm.get(evt).f_12_ENRC()) + #i0_data.append(ipm.get(evt).f_12_ENRC()) + i0_data.append(getattr(ipm.get(evt), ipm_det)()) except: logger.warning('missing i0 for event {}'.format(evt_idx)) i0_data.append(0.0) diff --git a/jet_tracking/mpi_scripts/mpi_configs/default_config.yml b/jet_tracking/mpi_scripts/mpi_configs/cxi_config.yml similarity index 100% rename from jet_tracking/mpi_scripts/mpi_configs/default_config.yml rename to jet_tracking/mpi_scripts/mpi_configs/cxi_config.yml diff --git a/jet_tracking/mpi_scripts/mpi_configs/xcs_config.yml b/jet_tracking/mpi_scripts/mpi_configs/xcs_config.yml new file mode 100644 index 0000000..8ec9418 --- /dev/null +++ b/jet_tracking/mpi_scripts/mpi_configs/xcs_config.yml @@ -0,0 +1,23 @@ +api_msg: + port: 5000 + +hutch: 'xcs' + +det_map: + name: 'epix10k2M' + shape: + - 1667 + - 1668 + dtype: float32 + bins: 100 + +pv_map: + 1: 'CXI:JTRK:REQ:DIFF_INTENSITY' + 2: 'CXI:JTRK:REQ:I0' + +ipm: + name: 'XCS-SB2-BMMON' + det: 'TotalIntensity' +#ipm: +# name: 'CXI-DG2-BMMON' +# det: None From ebe057d3bad152982b3f31fe0edba46991d1fcbf Mon Sep 17 00:00:00 2001 From: Adam Date: Sat, 13 Mar 2021 16:59:07 -0800 Subject: [PATCH 11/23] unused import --- jet_tracking/mpi_scripts/mpi_worker.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/jet_tracking/mpi_scripts/mpi_worker.py b/jet_tracking/mpi_scripts/mpi_worker.py index bbc5c50..5134f7e 100644 --- a/jet_tracking/mpi_scripts/mpi_worker.py +++ b/jet_tracking/mpi_scripts/mpi_worker.py @@ -14,8 +14,6 @@ import inspect from mpi4py import MPI -from smalldata_tools.SmallDataUtils import detData - f = '%(asctime)s - %(levelname)s - %(filename)s:%(funcName)s - %(message)s' logging.basicConfig(level=logging.DEBUG, format=f) logger = logging.getLogger(__name__) From 3ae700e3a6aeb36158ba296c30e609430333ae04 Mon Sep 17 00:00:00 2001 From: Adam Date: Sat, 13 Mar 2021 17:16:16 -0800 Subject: [PATCH 12/23] working xcs version --- jet_tracking/mpi_scripts/mpi_driver.py | 4 +- jet_tracking/mpi_scripts/mpi_master.py | 8 +- jet_tracking/mpi_scripts/mpi_worker.py | 2 +- jet_tracking/mpi_scripts/runMpiScript | 4 +- jet_tracking/psana/__init__.py | 1 - jet_tracking/psana/psana2epics.py | 381 ------------------------- jet_tracking/psana/psana2epics.sh | 26 -- jet_tracking/psana/psana2epics_sc3.py | 381 ------------------------- jet_tracking/psana/psana2epics_sc3.sh | 26 -- jet_tracking/psana/shmem_notes | 85 ------ 10 files changed, 9 insertions(+), 909 deletions(-) delete mode 100644 jet_tracking/psana/__init__.py delete mode 100644 jet_tracking/psana/psana2epics.py delete mode 100755 jet_tracking/psana/psana2epics.sh delete mode 100644 jet_tracking/psana/psana2epics_sc3.py delete mode 100755 jet_tracking/psana/psana2epics_sc3.sh delete mode 100644 jet_tracking/psana/shmem_notes diff --git a/jet_tracking/mpi_scripts/mpi_driver.py b/jet_tracking/mpi_scripts/mpi_driver.py index 94b80a2..90d171b 100644 --- a/jet_tracking/mpi_scripts/mpi_driver.py +++ b/jet_tracking/mpi_scripts/mpi_driver.py @@ -17,7 +17,7 @@ parser.add_argument('--exprun', help='psana experiment/run string (e.g. exp=xppd7114:run=43)', type=str, default='') #parser.add_argument('--dsname', help='data source name', type=str, default='') parser.add_argument('--nevts', help='number of events', default=50, type=int) -parser.add_argument('--cfg_file', help='if specified, has information about what metadata to use', type=str, default='default_config.yml') +parser.add_argument('--cfg_file', help='if specified, has information about what metadata to use', type=str, default='xcs_config.yml') args = parser.parse_args() # Two options for now, offline data or shared memory @@ -29,7 +29,7 @@ dsname = ''.join([args.exprun, ':smd:', 'dir=', exp_dir]) else: dsname = 'shmem=psana.0:stop=no' - psana.setOption('psana.calib-dir', '/reg/d/psdm/cxi/cxilv9518/calib/') + psana.setOption('psana.calib-dir', '/reg/d/psdm/xcs/xcsx39718/calib/') # Parse config file to hand to workers with open(''.join(['mpi_configs/', args.cfg_file])) as f: diff --git a/jet_tracking/mpi_scripts/mpi_master.py b/jet_tracking/mpi_scripts/mpi_master.py index 86bf061..10f8a39 100644 --- a/jet_tracking/mpi_scripts/mpi_master.py +++ b/jet_tracking/mpi_scripts/mpi_master.py @@ -137,9 +137,9 @@ def send_from_queue(self): #print('caputing data ', data) #for k, v in self._pv_map: #caput(v, data[k]) - ratio = data[1] / data[0] - caput('CXI:JTRK:REQ:DIFF_INTENSITY', data[1]) - caput('CXI:JTRK:REQ:I0', data[0]) - caput('CXI:JTRK:REQ:RATIO', ratio) + #ratio = data[1] / data[0] + caput('XCS:JTRK:REQ:DIFF_INTENSITY', data[1]) + caput('XCS:JTRK:REQ:I0', data[0]) + #caput('CXI:JTRK:REQ:RATIO', ratio) else: pass diff --git a/jet_tracking/mpi_scripts/mpi_worker.py b/jet_tracking/mpi_scripts/mpi_worker.py index 5134f7e..48765a3 100644 --- a/jet_tracking/mpi_scripts/mpi_worker.py +++ b/jet_tracking/mpi_scripts/mpi_worker.py @@ -113,7 +113,7 @@ def delta_bin(self, delta_bin): def start_run(self): """Worker should handle any calculations""" #mask_det = det.mask(188, unbond=True, unbondnbrs=True, status=True, edges=True, central=True) - ped = self.detector.pedestals(1)[0] + ped = self.detector.pedestals(48)[0] for evt_idx, evt in enumerate(self.ds.events()): if self.event_code not in self.evr.eventCodes(evt): continue diff --git a/jet_tracking/mpi_scripts/runMpiScript b/jet_tracking/mpi_scripts/runMpiScript index fa00b70..9b82e14 100755 --- a/jet_tracking/mpi_scripts/runMpiScript +++ b/jet_tracking/mpi_scripts/runMpiScript @@ -76,6 +76,6 @@ PROC=${PROC:='2'} source /reg/g/pcds/setup/pathmunge.sh source /reg/g/psdm/sw/conda1/manage/bin/psconda.sh -cd /reg/neh/home/aegger/smalldata_tools/mpi_scripts -pythonpathmunge '/reg/neh/home/aegger/smalldata_tools' +cd /cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/mpi_scripts +pythonpathmunge '/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking' `which mpirun` -n $PROC python mpi_driver.py $ARGS diff --git a/jet_tracking/psana/__init__.py b/jet_tracking/psana/__init__.py deleted file mode 100644 index df15f9d..0000000 --- a/jet_tracking/psana/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from .psana2epics import * # noqa diff --git a/jet_tracking/psana/psana2epics.py b/jet_tracking/psana/psana2epics.py deleted file mode 100644 index 4fbb4af..0000000 --- a/jet_tracking/psana/psana2epics.py +++ /dev/null @@ -1,381 +0,0 @@ -import argparse -import sys -import time - -import numpy as np -import pandas as pd -from epics import PV -from scipy.signal import peak_widths, periodogram - -time0 = time.time() - - -def initArgs(): - """Initialize argparse arguments. - """ - parser = argparse.ArgumentParser() - parser.add_argument("--calc_streak", action="store_true", default=False, - help='Calculate streak') - parser.add_argument("--calc_period", action="store_true", default=False, - help='Calculate periodogram') - parser.add_argument("--plot", action="store_true", default=False, - help='Plot normalized spectrum') - parser.add_argument("--nevents", type=int, default=10, - help='Number of events to average') - parser.add_argument("--exp", type=str, default='cxilr6716', - help='Experiment') - parser.add_argument("--run", type=int, - help='Run') - parser.add_argument("--instrument", type=str, default='cxi', - help='Instrument') - parser.add_argument("--pvbase", type=str, default='CXI:SC1:DIFFRACT', - help='pvbase') - parser.add_argument("--alias", type=str, default='DscCsPad', - help='detector alias') - return parser.parse_args() - - -def DataSource(exp=None, run=None, **kwargs): - """ - Wrapper for loading PyDataSource DataSource - """ - import PyDataSource - if exp and run: - print('Loading DataSource for {:} run {:}'.format(exp, run)) - ds = PyDataSource.DataSource(exp=exp, run=int(run)) - elif exp: - print('Loading DataSource for shared memory with expiment {:}' - ''.format(exp)) - ds = PyDataSource.DataSource(exp=exp) - else: - print('Loading DataSource for shared memory') - ds = PyDataSource.DataSource() - - print(ds.configData.show_info()) - print('') - print('Load time: {:} sec'.format(time.time() - time0)) - return ds - - -def output_cspad_sum(ds=None, alias='DscCsPad', - pvbase='CXI:SC1:DIFFRACT', calc_period=True, calc_streak=False, - psd_events=None, psd_rate=None, psd_resolution=None, **kwargs): - """Outputs cspad sum and certain statistics as PVs - - Parameters - ---------- - ds : DataSource, optional - DataSource object, if not specified, loads it using kwargs - alias : str, optional - Name for CsPad data - pvbase : str, optional - Base for PV names - calc_period : bool, optional - Determines the execution of frequency analysis - psd_events : int, optional - Number of events for frequency analysis, default is 240 - psd_rate : int or float, optional - Event rate [Hz], default is 120 - psd_resolution : int, optional - Resolution setting will perform rolling mean [Hz] - """ - - # Configure epics PVs - print('Initializing epics PVs') - cspad_sum_pv = PV(':'.join([pvbase, 'TOTAL_ADU'])) - streak_fraction_pv = PV(':'.join([pvbase, 'STREAK_FRACTION'])) - stats_mean_pv = PV(':'.join([pvbase, 'STATS_MEAN'])) - stats_std_pv = PV(':'.join([pvbase, 'STATS_STD'])) - stats_min_pv = PV(':'.join([pvbase, 'STATS_MIN'])) - stats_max_pv = PV(':'.join([pvbase, 'STATS_MAX'])) - psd_frequency_pv = PV(':'.join([pvbase, 'PSD_FREQUENCY'])) - psd_amplitude_pv = PV(':'.join([pvbase, 'PSD_AMPLITUDE'])) - psd_rate_pv = PV(':'.join([pvbase, 'PSD_RATE'])) - psd_events_pv = PV(':'.join([pvbase, 'PSD_EVENTS'])) - psd_resolution_pv = PV(':'.join([pvbase, 'PSD_RESOLUTION'])) - psd_freq_min_pv = PV(':'.join([pvbase, 'PSD_FREQ_MIN'])) - psd_freq_wf_pv = PV(':'.join([pvbase, 'PSD_FREQ_WF'])) - psd_amp_wf_pv = PV(':'.join([pvbase, 'PSD_AMP_WF'])) - # psd_amp_array_pv = PV(':'.join([pvbase,'PSD_AMP_ARRAY'])) - - if psd_rate: - psd_rate_pv.put(psd_rate) - - psd_rate = psd_rate_pv.get() - if psd_rate > 360 or psd_rate < 10: - psd_rate = 120. - psd_rate_pv.put(psd_rate) - - if psd_events: - psd_events_pv.put(psd_events) - - psd_events = psd_events_pv.get() - if psd_events > 1200 or psd_events < 60: - psd_events = psd_rate * 2. - psd_events_pv.put(psd_events) - - if psd_resolution: - psd_resolution_pv.put(psd_resolution) - - psd_resolution = psd_resolution_pv.get() - if psd_resolution > 5 or psd_resolution < 0.1: - psd_resolution = psd_rate / float(psd_events) - psd_resolution_pv.put(psd_resolution) - - nroll = int(psd_resolution * psd_events / float(psd_rate)) - - psd_freq_min = psd_freq_min_pv.get() - if psd_freq_min > 40 or psd_freq_min < 2: - psd_freq_min = 5. - psd_freq_min_pv.put(psd_freq_min) - - if0 = int(psd_freq_min / float(psd_rate) * psd_events) - - psd_freq_wf = np.arange(psd_events / 2. + 1.) * \ - float(psd_rate) / float(psd_events) - psd_freq_wf_pv.put(psd_freq_wf) - - print('Events = {}'.format(psd_events)) - - print('... done') - - if not ds: - ds = DataSource(**kwargs) - print('... done') - - detector = ds._detectors[alias] - - detector.next() - detector.add.property(asic) - detector.add.property(streak_present) - try: - no_streak = [] - iloop = 0 - icheck = 0 - streaks = 0 - time0 = time.time() - time_last = time0 - sums = [] - # aPxx = [] - # atime = [] - while True: - cspad_sum = detector.corr.sum() - sums.append(cspad_sum) - cspad_sum_pv.put(cspad_sum) - if calc_streak: - streak = detector.streak_present - streaks += streak - if not streak: - no_streak.append(iloop) - - iloop += 1 - icheck += 1 - if not iloop % psd_events: - sums = np.asarray(sums) - det_avg = sums.mean() - det_std = sums.std() - det_max = sums.max() - det_min = sums.min() - stats_mean_pv.put(det_avg) - stats_max_pv.put(det_max) - stats_min_pv.put(det_min) - stats_std_pv.put(det_std) - - if calc_period: - # f should be same as psd_freq_wf - f, Pxx = periodogram(sums, psd_rate) - if nroll > 1: - Pxx = pd.DataFrame(Pxx).rolling( - nroll).mean().values[nroll:, 0] - f = f[nroll:] - psd_frequency = f[Pxx[if0:].argmax() + if0] - psd_amplitude = Pxx[if0:].max() / 4 * psd_rate / psd_events - psd_frequency_pv.put(psd_frequency) - psd_amplitude_pv.put(psd_amplitude) - psd_amp_wf_pv.put(Pxx) - time_next = time.time() - evtrate = icheck / (time_next - time_last) - icheck = 0 - time_last = time_next - print('{:8.1f} Hz - {:8.1f} {:12} {:12} {:12}' - ''.format(evtrate, psd_frequency, psd_amplitude, - det_avg, det_std)) -# -# Need to makd sure right shape before outputting array -# aPxx.append(Pxx) -# psd_amp_array_pv.put(np.asarray(aPxx)) - - if calc_streak: - streak_fraction = streaks / psd_events - streak_fraction_pv.put(streak_fraction) - - sums = [] - # aPxx = [] - # atime = [] - streaks = 0 - no_streak = [] - - # Change to evt.next() in future and count damage - detector.next() - - except KeyboardInterrupt: - return - except Exception as e: - print(e) - - -def output_cspad_streak(ds=None, alias='DscCsPad', - pvbase='CXI:SC1:DIFFRACT', nevents=10, **kwargs): - """ - Output cspad jet streak information - """ - - beam_x_pv = PV(':'.join([pvbase, 'X0'])) - beam_y_pv = PV(':'.join([pvbase, 'Y0'])) - streak_angle_pv = PV(':'.join([pvbase, 'STREAK_PHI'])) - streak_intensity_pv = PV(':'.join([pvbase, 'STREAK_INTENSITY'])) - streak_width_pv = PV(':'.join([pvbase, 'STREAK_WIDTH'])) - if not ds: - ds = DataSource(**kwargs) - -# Now set in epics -- update as needed from epics. -# beam_x_pv.put(2094.9301668334006) # run 104 -# beam_y_pv.put(-1796.5697333657126) - - detector = ds._detectors[alias] - detector.next() - - detector.add.property(asic) - cy, cx = get_center(detector, beam_x_pv, beam_y_pv) - j_map_1, j_map_2 = find_proj_mapping(cy, cx) - detector.add.parameter(proj_map_1=j_map_1, proj_map_2=j_map_2) - detector.add.property(streak_angle_raw) - detector.add.property(streak_present) - try: - iloop = 0 - time0 = time.time() - while True: - streak_angle = detector.streak_angle_raw[0] - streak_intensity = detector.streak_angle_raw[1] - streak_width = detector.streak_angle_raw[2] - streak_angle_pv.put(streak_angle) - streak_intensity_pv.put(streak_intensity) - streak_width_pv.put(streak_width) - if not (iloop + 1) % nevents and detector.streak_present: - evt_rate = iloop / (time.time() - time0) - print('{:15} {:6.1f} Hz {:5.1f} {:5.1f} {:5.3f} {}' - ''.format(iloop, evt_rate, streak_angle, - streak_intensity, streak_width, - int(detector.streak_present))) - iloop += 1 - detector.next() - - except KeyboardInterrupt: - return - - -def streak_present(self): - im1 = self.asic[0] - im2 = self.asic[2] - return streak_present_im(im1) and streak_present_im(im2) - - -def streak_present_im(im): - '''im is 2D np-array''' - s = im[-10:].sum(axis=0) - s -= s.mean() - s /= np.roll(s, 10 - s.argmax())[20:].std() - return s.max() > 5 - - -def get_center(self, x0_pv, y0_pv): - center = (y0_pv.get(), x0_pv.get()) - cy, cx = get_center_coords(self, center) - cy -= 185 - return cy, cx - - -def to_pad_coord(det, point, i): - '''Point: (y,x)''' - - pad = [1, 9, 17, 25][i] - origin = np.asarray( - (det.calibData.coords_x[pad, 0, 0], det.calibData.coords_y[pad, 0, 0])) - unit_y = ((det.calibData.coords_x[pad, 1, 0] - det.calibData.coords_x[pad, 0, 0]), - (det.calibData.coords_y[pad, 1, 0] - det.calibData.coords_y[pad, 0, 0])) - unit_x = ((det.calibData.coords_x[pad, 0, 1] - det.calibData.coords_x[pad, 0, 0]), - (det.calibData.coords_y[pad, 0, 1] - det.calibData.coords_y[pad, 0, 0])) - matrix = np.asarray([[unit_y[0], unit_x[0]], [unit_y[1], unit_x[1]]]) - pos = np.linalg.solve(matrix, np.asarray(point) - origin) - return pos - - -def get_center_coords(det, center): - cy = np.zeros(4) - cx = np.zeros(4) - for i in range(4): - pos = to_pad_coord(det, center, i) - cy[i], cx[i] = pos[0], pos[1] - return cy, cx - - -def find_proj_mapping(cy, cx): - sq = 0 - - j_index_1 = np.zeros((100, 80), dtype=np.int64) - j_index_2 = np.zeros((100, 80), dtype=np.int64) - for a in range(-40, 40): - ang = np.radians(float(a) / 2) - for i in range(100): - j = int(np.tan(ang) * (100 - i + cy[sq]) + cx[sq]) % 100 - j_index_1[i, a + 40] = j - j = int(np.tan(ang) * - (100 - i + cy[(sq + 2) % 4]) + cx[(sq + 2) % 4]) % 100 - j_index_2[i, a + 40] = j - return j_index_1, j_index_2 - - -def asic(self, attr='corr'): - """ - Select inner asics - """ - return getattr(self, attr)[[1, 9, 17, 25], :, 0:194] - - -def streak_angle_raw(self): - """ - Jet streak calculation - Returns: jet angle, jet intensity (as standard deviations from the mean), - jet width - - """ - sq = 0 - - asic = self.asic - im1 = asic[sq][-100:, :100] - im2 = asic[(sq + 2) % 4][-100:, :100] - proj1 = np.zeros((100, 80)) - proj2 = np.zeros((100, 80)) - for a in range(-40, 40): - for i in range(im1.shape[0]): - proj1[i, a + 40] = im1[i, self.proj_map_1[i, a + 40]] - proj2[i, a + 40] = im2[i, self.proj_map_2[i, a + 40]] - s = proj1.sum(axis=0) + proj2.sum(axis=0) - s -= s.mean() - s /= np.roll(s, 10 - s.argmax())[20:].std() - peak = s[1:-1].argmax() + 1 - try: - peakwidth = peak_widths(s, [peak])[0][0] - except Exception: - peakwidth = 5 - return (np.pi * (peak - 40) / 360.0, s.max(), peakwidth) - - -if __name__ == "__main__": - args = initArgs() - print('Initializing args: {}'.format(args)) - sys.exit(output_cspad_sum(alias=args.alias, pvbase=args.pvbase, - exp=args.exp, run=args.run, - calc_period=args.calc_period, - calc_streak=args.calc_streak, - nevents=args.nevents, plot=args.plot)) diff --git a/jet_tracking/psana/psana2epics.sh b/jet_tracking/psana/psana2epics.sh deleted file mode 100755 index 71439cd..0000000 --- a/jet_tracking/psana/psana2epics.sh +++ /dev/null @@ -1,26 +0,0 @@ -#!/bin/bash - -unset PYTHONPATH -unset LD_LIBRARY_PATH - -export set EPICS_SITE_CONFIG=/reg/g/pcds/package/epics/3.14/RELEASE_SITE -source /reg/g/pcds/setup/epicsenv-cur.sh -export EPICS_CA_MAX_ARRAY_BYTES=12000000 - -source /reg/g/psdm/etc/psconda.sh > /dev/null - -SOURCE="${BASH_SOURCE[0]}" -# resolve $SOURCE until the file is no longer a symlink -while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located -done - -DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" - -cd $DIR - -args="$@" -python psana2epics.py $args diff --git a/jet_tracking/psana/psana2epics_sc3.py b/jet_tracking/psana/psana2epics_sc3.py deleted file mode 100644 index a7115e8..0000000 --- a/jet_tracking/psana/psana2epics_sc3.py +++ /dev/null @@ -1,381 +0,0 @@ -import argparse -import sys -import time - -import numpy as np -import pandas as pd -from epics import PV -from scipy.signal import peak_widths, periodogram - -time0 = time.time() - - -def initArgs(): - """Initialize argparse arguments. - """ - parser = argparse.ArgumentParser() - parser.add_argument("--calc_streak", action="store_true", default=False, - help='Calculate streak') - parser.add_argument("--calc_period", action="store_true", default=False, - help='Calculate periodogram') - parser.add_argument("--plot", action="store_true", default=False, - help='Plot normalized spectrum') - parser.add_argument("--nevents", type=int, default=10, - help='Number of events to average') - parser.add_argument("--exp", type=str, default='cxix34517', - help='Experiment') - parser.add_argument("--run", type=int, - help='Run') - parser.add_argument("--instrument", type=str, default='cxi', - help='Instrument') - parser.add_argument("--pvbase", type=str, default='CXI:SC3:DIFFRACT', - help='pvbase') - parser.add_argument("--alias", type=str, default='DsdCsPad', - help='detector alias') - return parser.parse_args() - - -def DataSource(exp=None, run=None, **kwargs): - """ - Wrapper for loading PyDataSource DataSource - """ - import PyDataSource - if exp and run: - print('Loading DataSource for {:} run {:}'.format(exp, run)) - ds = PyDataSource.DataSource(exp=exp, run=int(run)) - elif exp: - print('Loading DataSource for shared memory with expiment {:}' - ''.format(exp)) - ds = PyDataSource.DataSource(exp=exp) - else: - print('Loading DataSource for shared memory') - ds = PyDataSource.DataSource() - - print(ds.configData.show_info()) - print('') - print('Load time: {:} sec'.format(time.time() - time0)) - return ds - - -def output_cspad_sum(ds=None, alias='DsdCsPad', - pvbase='CXI:SC3:DIFFRACT', calc_period=True, calc_streak=False, - psd_events=None, psd_rate=None, psd_resolution=None, **kwargs): - """Outputs cspad sum and certain statistics as PVs - - Parameters - ---------- - ds : DataSource, optional - DataSource object, if not specified, loads it using kwargs - alias : str, optional - Name for CsPad data - pvbase : str, optional - Base for PV names - calc_period : bool, optional - Determines the execution of frequency analysis - psd_events : int, optional - Number of events for frequency analysis, default is 240 - psd_rate : int or float, optional - Event rate [Hz], default is 120 - psd_resolution : int, optional - Resolution setting will perform rolling mean [Hz] - """ - - # Configure epics PVs - print('Initializing epics PVs') - cspad_sum_pv = PV(':'.join([pvbase, 'TOTAL_ADU'])) - streak_fraction_pv = PV(':'.join([pvbase, 'STREAK_FRACTION'])) - stats_mean_pv = PV(':'.join([pvbase, 'STATS_MEAN'])) - stats_std_pv = PV(':'.join([pvbase, 'STATS_STD'])) - stats_min_pv = PV(':'.join([pvbase, 'STATS_MIN'])) - stats_max_pv = PV(':'.join([pvbase, 'STATS_MAX'])) - psd_frequency_pv = PV(':'.join([pvbase, 'PSD_FREQUENCY'])) - psd_amplitude_pv = PV(':'.join([pvbase, 'PSD_AMPLITUDE'])) - psd_rate_pv = PV(':'.join([pvbase, 'PSD_RATE'])) - psd_events_pv = PV(':'.join([pvbase, 'PSD_EVENTS'])) - psd_resolution_pv = PV(':'.join([pvbase, 'PSD_RESOLUTION'])) - psd_freq_min_pv = PV(':'.join([pvbase, 'PSD_FREQ_MIN'])) - psd_freq_wf_pv = PV(':'.join([pvbase, 'PSD_FREQ_WF'])) - psd_amp_wf_pv = PV(':'.join([pvbase, 'PSD_AMP_WF'])) - # psd_amp_array_pv = PV(':'.join([pvbase,'PSD_AMP_ARRAY'])) - - if psd_rate: - psd_rate_pv.put(psd_rate) - - psd_rate = psd_rate_pv.get() - if psd_rate > 360 or psd_rate < 10: - psd_rate = 120. - psd_rate_pv.put(psd_rate) - - if psd_events: - psd_events_pv.put(psd_events) - - psd_events = psd_events_pv.get() - if psd_events > 1200 or psd_events < 60: - psd_events = psd_rate * 2. - psd_events_pv.put(psd_events) - - if psd_resolution: - psd_resolution_pv.put(psd_resolution) - - psd_resolution = psd_resolution_pv.get() - if psd_resolution > 5 or psd_resolution < 0.1: - psd_resolution = psd_rate / float(psd_events) - psd_resolution_pv.put(psd_resolution) - - nroll = int(psd_resolution * psd_events / float(psd_rate)) - - psd_freq_min = psd_freq_min_pv.get() - if psd_freq_min > 40 or psd_freq_min < 2: - psd_freq_min = 5. - psd_freq_min_pv.put(psd_freq_min) - - if0 = int(psd_freq_min / float(psd_rate) * psd_events) - - psd_freq_wf = np.arange(psd_events / 2. + 1.) * \ - float(psd_rate) / float(psd_events) - psd_freq_wf_pv.put(psd_freq_wf) - - print('Events = {}'.format(psd_events)) - - print('... done') - - if not ds: - ds = DataSource(**kwargs) - print('... done') - - detector = ds._detectors[alias] - - detector.next() - detector.add.property(asic) - detector.add.property(streak_present) - try: - no_streak = [] - iloop = 0 - icheck = 0 - streaks = 0 - time0 = time.time() - time_last = time0 - sums = [] - # aPxx = [] - # atime = [] - while True: - cspad_sum = detector.corr.sum() - sums.append(cspad_sum) - cspad_sum_pv.put(cspad_sum) - if calc_streak: - streak = detector.streak_present - streaks += streak - if not streak: - no_streak.append(iloop) - - iloop += 1 - icheck += 1 - if not iloop % psd_events: - sums = np.asarray(sums) - det_avg = sums.mean() - det_std = sums.std() - det_max = sums.max() - det_min = sums.min() - stats_mean_pv.put(det_avg) - stats_max_pv.put(det_max) - stats_min_pv.put(det_min) - stats_std_pv.put(det_std) - - if calc_period: - # f should be same as psd_freq_wf - f, Pxx = periodogram(sums, psd_rate) - if nroll > 1: - Pxx = pd.DataFrame(Pxx).rolling( - nroll).mean().values[nroll:, 0] - f = f[nroll:] - psd_frequency = f[Pxx[if0:].argmax() + if0] - psd_amplitude = Pxx[if0:].max() / 4 * psd_rate / psd_events - psd_frequency_pv.put(psd_frequency) - psd_amplitude_pv.put(psd_amplitude) - psd_amp_wf_pv.put(Pxx) - time_next = time.time() - evtrate = icheck / (time_next - time_last) - icheck = 0 - time_last = time_next - print('{:8.1f} Hz - {:8.1f} {:12} {:12} {:12}' - ''.format(evtrate, psd_frequency, psd_amplitude, - det_avg, det_std)) -# -# Need to makd sure right shape before outputting array -# aPxx.append(Pxx) -# psd_amp_array_pv.put(np.asarray(aPxx)) - - if calc_streak: - streak_fraction = streaks / psd_events - streak_fraction_pv.put(streak_fraction) - - sums = [] - # aPxx = [] - # atime = [] - streaks = 0 - no_streak = [] - - # Change to evt.next() in future and count damage - detector.next() - - except KeyboardInterrupt: - return - except Exception as e: - print(e) - - -def output_cspad_streak(ds=None, alias='DsdCsPad', - pvbase='CXI:SC3:DIFFRACT', nevents=10, **kwargs): - """ - Output cspad jet streak information - """ - - beam_x_pv = PV(':'.join([pvbase, 'X0'])) - beam_y_pv = PV(':'.join([pvbase, 'Y0'])) - streak_angle_pv = PV(':'.join([pvbase, 'STREAK_PHI'])) - streak_intensity_pv = PV(':'.join([pvbase, 'STREAK_INTENSITY'])) - streak_width_pv = PV(':'.join([pvbase, 'STREAK_WIDTH'])) - if not ds: - ds = DataSource(**kwargs) - -# Now set in epics -- update as needed from epics. -# beam_x_pv.put(2094.9301668334006) # run 104 -# beam_y_pv.put(-1796.5697333657126) - - detector = ds._detectors[alias] - detector.next() - - detector.add.property(asic) - cy, cx = get_center(detector, beam_x_pv, beam_y_pv) - j_map_1, j_map_2 = find_proj_mapping(cy, cx) - detector.add.parameter(proj_map_1=j_map_1, proj_map_2=j_map_2) - detector.add.property(streak_angle_raw) - detector.add.property(streak_present) - try: - iloop = 0 - time0 = time.time() - while True: - streak_angle = detector.streak_angle_raw[0] - streak_intensity = detector.streak_angle_raw[1] - streak_width = detector.streak_angle_raw[2] - streak_angle_pv.put(streak_angle) - streak_intensity_pv.put(streak_intensity) - streak_width_pv.put(streak_width) - if not (iloop + 1) % nevents and detector.streak_present: - evt_rate = iloop / (time.time() - time0) - print('{:15} {:6.1f} Hz {:5.1f} {:5.1f} {:5.3f} {}' - ''.format(iloop, evt_rate, streak_angle, - streak_intensity, streak_width, - int(detector.streak_present))) - iloop += 1 - detector.next() - - except KeyboardInterrupt: - return - - -def streak_present(self): - im1 = self.asic[0] - im2 = self.asic[2] - return streak_present_im(im1) and streak_present_im(im2) - - -def streak_present_im(im): - '''im is 2D np-array''' - s = im[-10:].sum(axis=0) - s -= s.mean() - s /= np.roll(s, 10 - s.argmax())[20:].std() - return s.max() > 5 - - -def get_center(self, x0_pv, y0_pv): - center = (y0_pv.get(), x0_pv.get()) - cy, cx = get_center_coords(self, center) - cy -= 185 - return cy, cx - - -def to_pad_coord(det, point, i): - '''Point: (y,x)''' - - pad = [1, 9, 17, 25][i] - origin = np.asarray( - (det.calibData.coords_x[pad, 0, 0], det.calibData.coords_y[pad, 0, 0])) - unit_y = ((det.calibData.coords_x[pad, 1, 0] - det.calibData.coords_x[pad, 0, 0]), - (det.calibData.coords_y[pad, 1, 0] - det.calibData.coords_y[pad, 0, 0])) - unit_x = ((det.calibData.coords_x[pad, 0, 1] - det.calibData.coords_x[pad, 0, 0]), - (det.calibData.coords_y[pad, 0, 1] - det.calibData.coords_y[pad, 0, 0])) - matrix = np.asarray([[unit_y[0], unit_x[0]], [unit_y[1], unit_x[1]]]) - pos = np.linalg.solve(matrix, np.asarray(point) - origin) - return pos - - -def get_center_coords(det, center): - cy = np.zeros(4) - cx = np.zeros(4) - for i in range(4): - pos = to_pad_coord(det, center, i) - cy[i], cx[i] = pos[0], pos[1] - return cy, cx - - -def find_proj_mapping(cy, cx): - sq = 0 - - j_index_1 = np.zeros((100, 80), dtype=np.int64) - j_index_2 = np.zeros((100, 80), dtype=np.int64) - for a in range(-40, 40): - ang = np.radians(float(a) / 2) - for i in range(100): - j = int(np.tan(ang) * (100 - i + cy[sq]) + cx[sq]) % 100 - j_index_1[i, a + 40] = j - j = int(np.tan(ang) * - (100 - i + cy[(sq + 2) % 4]) + cx[(sq + 2) % 4]) % 100 - j_index_2[i, a + 40] = j - return j_index_1, j_index_2 - - -def asic(self, attr='corr'): - """ - Select inner asics - """ - return getattr(self, attr)[[1, 9, 17, 25], :, 0:194] - - -def streak_angle_raw(self): - """ - Jet streak calculation - Returns: jet angle, jet intensity (as standard deviations from the mean), - jet width - - """ - sq = 0 - - asic = self.asic - im1 = asic[sq][-100:, :100] - im2 = asic[(sq + 2) % 4][-100:, :100] - proj1 = np.zeros((100, 80)) - proj2 = np.zeros((100, 80)) - for a in range(-40, 40): - for i in range(im1.shape[0]): - proj1[i, a + 40] = im1[i, self.proj_map_1[i, a + 40]] - proj2[i, a + 40] = im2[i, self.proj_map_2[i, a + 40]] - s = proj1.sum(axis=0) + proj2.sum(axis=0) - s -= s.mean() - s /= np.roll(s, 10 - s.argmax())[20:].std() - peak = s[1:-1].argmax() + 1 - try: - peakwidth = peak_widths(s, [peak])[0][0] - except Exception: - peakwidth = 5 - return (np.pi * (peak - 40) / 360.0, s.max(), peakwidth) - - -if __name__ == "__main__": - args = initArgs() - print('Initializing args: {}'.format(args)) - sys.exit(output_cspad_sum(alias=args.alias, pvbase=args.pvbase, - exp=args.exp, run=args.run, - calc_period=args.calc_period, - calc_streak=args.calc_streak, - nevents=args.nevents, plot=args.plot)) diff --git a/jet_tracking/psana/psana2epics_sc3.sh b/jet_tracking/psana/psana2epics_sc3.sh deleted file mode 100755 index 1e00816..0000000 --- a/jet_tracking/psana/psana2epics_sc3.sh +++ /dev/null @@ -1,26 +0,0 @@ -#!/bin/bash - -unset PYTHONPATH -unset LD_LIBRARY_PATH - -export set EPICS_SITE_CONFIG=/reg/g/pcds/package/epics/3.14/RELEASE_SITE -source /reg/g/pcds/setup/epicsenv-cur.sh -export EPICS_CA_MAX_ARRAY_BYTES=12000000 - -source /reg/g/psdm/etc/psconda.sh > /dev/null - -SOURCE="${BASH_SOURCE[0]}" -# resolve $SOURCE until the file is no longer a symlink -while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located -done - -DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" - -cd $DIR - -args="$@" -python psana2epics_sc3.py $args diff --git a/jet_tracking/psana/shmem_notes b/jet_tracking/psana/shmem_notes deleted file mode 100644 index 265bbde..0000000 --- a/jet_tracking/psana/shmem_notes +++ /dev/null @@ -1,85 +0,0 @@ -Notes for auto jet tracking - -See HXR Jet Tracking google drive for project notes: -- https://drive.google.com/drive/folders/1TJdb9qK85oxeFpoPQ5m080HZw-Dptm7e - -Shared memory application analysis based on GDVN for cxilr6716: -- see also: /reg/neh/operator/cxiopr/experiments/cxilr6716/src/README - -pvNotepad pvs hosted by the ioc-mfx-cspadPV ioc: -/reg/g/pcds/package/epics/3.14-dev/ioc/mfx/pvNotepad/current/ioc-mfx-cspadPV.cfg - ------------------------ -Running psana with output to shared memory - -psana2epics.sh example will output the sum of the CSPAD intensity to a PV. - -e.g., for start of Run 17 we are using SC2 - -[koglin@daq-cxi-mon01 ~ 09:34:39] /reg/g/pcds/pyps/apps/hutch-python/cxi/cxi/jet_tracking/psana/psana2epics.sh --alias='DsaCsPad' --pvbase='CXI:SC2:DIFFRACT' -Initializing args Namespace(alias='DsaCsPad', calc_period=False, calc_streak=False, exp='cxilr6716', instrument='cxi', nevents=10, plot=False, pvbase='CXI:SC2:DIFFRACT', run=None) -Initializing epics PVs -Events = 240.0 -... done -Loading DataSource for shared memory with expiment cxilr6716 -No data source specified, so assume this is shared memory. -setting calibDir cxilr6716 /reg/d/psdm/cxi/cxilr6716/calib -Opened queue /PdsFromMonitorDiscovery_psana (9) -Opening shared memory /PdsMonitorSharedMemory_psana of size 0x4c800000 (0x22 * 0x2400000) -Shared memory at 0x7f7c473dc000 -Opened queue /PdsToMonitorEvQueue_psana_0 (21) -Opened queue /PdsToMonitorEvQueue_psana_1 (22) --------------------------------------------------------------------------------- -Source Information: ------------------- -*Detectors in group 0 are "BLD" data recorded at 120 Hz on event code 40 -*Detectors listed as Controls are controls devices with unknown event code (but likely 40). - -Alias Grp Description Code Pol Delay [s] Width [s] Source ------------------------------------------------------------------------------------------------------- -CXI_DG2_BMMON 1 BldInfo(CXI-DG2-BMMON) -DsaCsPad 1 120 Hz 40 Neg 0.000790723 0.000040000 DetInfo(CxiDs2.0:Cspad.0) -EBeam 1 BldInfo(EBeam) -FEEGasDetEnergy 1 BldInfo(FEEGasDetEnergy) -HFX_DG2_BMMON 1 BldInfo(HFX-DG2-BMMON) -HX2_SB1_BMMON 1 BldInfo(HX2-SB1-BMMON) -KbEncoder 1 120 Hz 40 Pos 0.000490723 0.000010000 DetInfo(CxiEndstation.0:USDUSB.0) -PhaseCavity 1 BldInfo(PhaseCavity) -Sc2Inline 1 120 Hz 40 Pos 0.000790723 0.007000000 DetInfo(CxiSc2.0:Opal1000.0) -XCS_SB1_BMMON 1 BldInfo(XCS-SB1-BMMON) --------------------------------------------------------------------------------- -Event Code Information: ------------------- -code group type description ----------------------------------------------------------- - 40 1 Readout 120 Hz - -Load time: 11.4506380558 sec -... done --------------------------------------------------------------------------- - - - -For CXI, monitor PV from cxi control room machine - -cxi-daq:cxi> camonitor CXI:SC2:DIFFRACT:TOTAL_ADU -CXI:SC2:DIFFRACT:TOTAL_ADU 2018-09-06 21:35:01.535993 5.33097e+06 -CXI:SC2:DIFFRACT:TOTAL_ADU 2018-09-06 21:35:01.579956 4.1387e+06 -CXI:SC2:DIFFRACT:TOTAL_ADU 2018-09-06 21:35:01.591779 4.3779e+06 -CXI:SC2:DIFFRACT:TOTAL_ADU 2018-09-06 21:35:01.603362 4.53231e+06 -CXI:SC2:DIFFRACT:TOTAL_ADU 2018-09-06 21:35:01.614737 3.38e+06 -... - -cxi-daq:cxi> caEventRate CXI:SC2:DIFFRACT:TOTAL_ADU.VAL -Connecting to CA Channel "CXI:SC2:DIFFRACT:TOTAL_ADU.VAL" 1 times. done(0.028546 sec). -Subscribing 1 times. done(0.000059 sec). -Waiting for initial value events. done(0.010099 sec). -CA Event Rate (Hz): current 40.9977 mean 40.9977 std dev 0 -CA Event Rate (Hz): current 39.4983 mean 40.248 std dev 0.749664 -CA Event Rate (Hz): current 38.4994 mean 39.6651 std dev 1.02671 -... - - -For mfx on daq-mfx-mon02: - -daq-mfx-mon02> /reg/g/pcds/pyps/apps/hutch-python/mfx/mfx/jet_tracking/psana/psana2epics.sh --alias='Rayonix' --pvbase='MFX:DET:DIFFRACT' --exp='mfxlt3017' From b251e77a53f4f1dbcd7926fce48f5796c45d260c Mon Sep 17 00:00:00 2001 From: Adam Date: Wed, 14 Apr 2021 08:48:54 -0700 Subject: [PATCH 13/23] move configs to generally accessible place, fix arp bash script --- .../jet_tracking_cal/submit_jt_arp.sh | 5 -- .../jet_tracking_cal/submit_jt_cal_arp.sh | 71 +++++++++++++++++++ .../mpi_configs => jt_configs}/cxi_config.yml | 0 .../mpi_configs => jt_configs}/xcs_config.yml | 5 +- jet_tracking/mpi_scripts/mpi_worker.py | 2 +- 5 files changed, 75 insertions(+), 8 deletions(-) delete mode 100755 jet_tracking/jet_tracking_cal/submit_jt_arp.sh create mode 100755 jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh rename jet_tracking/{mpi_scripts/mpi_configs => jt_configs}/cxi_config.yml (100%) rename jet_tracking/{mpi_scripts/mpi_configs => jt_configs}/xcs_config.yml (74%) diff --git a/jet_tracking/jet_tracking_cal/submit_jt_arp.sh b/jet_tracking/jet_tracking_cal/submit_jt_arp.sh deleted file mode 100755 index d6efc45..0000000 --- a/jet_tracking/jet_tracking_cal/submit_jt_arp.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -source /reg/g/psdm/sw/conda1/manage/bin/psconda.sh -ABS_PATH=/cds/home/a/aegger/jet_tracking/jet_tracking/jet_tracking_cal -sbatch --nodes=2 --time=5 $ABS_PATH/jt_cal.py "$@" diff --git a/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh b/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh new file mode 100755 index 0000000..013ccc3 --- /dev/null +++ b/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh @@ -0,0 +1,71 @@ +#!/bin/bash + +usage() +{ +cat << EOF +$(basename "$0"): + Script to launch a smalldata_tools run analysis + + OPTIONS: + -h|--help + Definition of options + -q|--queue + Queue to use on SLURM + -t|--tasks + Number of parallel tasks + -s|--script + Script to run with full path + -c|--config + Configuration file you want to use for jt cal +EOF + +} + +source /reg/g/psdm/etc/psconda.sh + +# Use getopts when we get a chance +POSITIONAL=() +while [[ $# -gt 0 ]] +do + key="$1" + + case $key in + -h|--help) + usage + exit + ;; + -q|--queue) + QUEUE="$2" + shift + shift + ;; + -t|--tasks) + TASKS="$2" + shift + shift + ;; + -s|--script) + SCRIPT="$2" + shift + shift + ;; + -c|--config) + CONFIG="$2" + shift + shift + ;; + *) + POSITIONAL+=("$1") + shift + ;; + esac +done +set -- "${POSITIONAL[@]}" + +# Need to setup for FFB +QUEUE=${QUEUE:='psanaq'} +TASKS=${TASKS:=10} +SCRIPT=${SCRIPT:=/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/jet_tracking_cal/jt_cal.py} +CONFIG=${CONFIG:=/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/jt_configs/xcs_config.yml} + +sbatch -p $QUEUE --ntasks $TASKS --wrap="mpirun python -u $SCRIPT $CONFIG" diff --git a/jet_tracking/mpi_scripts/mpi_configs/cxi_config.yml b/jet_tracking/jt_configs/cxi_config.yml similarity index 100% rename from jet_tracking/mpi_scripts/mpi_configs/cxi_config.yml rename to jet_tracking/jt_configs/cxi_config.yml diff --git a/jet_tracking/mpi_scripts/mpi_configs/xcs_config.yml b/jet_tracking/jt_configs/xcs_config.yml similarity index 74% rename from jet_tracking/mpi_scripts/mpi_configs/xcs_config.yml rename to jet_tracking/jt_configs/xcs_config.yml index 8ec9418..a963401 100644 --- a/jet_tracking/mpi_scripts/mpi_configs/xcs_config.yml +++ b/jet_tracking/jt_configs/xcs_config.yml @@ -2,6 +2,7 @@ api_msg: port: 5000 hutch: 'xcs' +experiment: 'xcsx39718' det_map: name: 'epix10k2M' @@ -12,8 +13,8 @@ det_map: bins: 100 pv_map: - 1: 'CXI:JTRK:REQ:DIFF_INTENSITY' - 2: 'CXI:JTRK:REQ:I0' + 1: 'XCS:JTRK:REQ:DIFF_INTENSITY' + 2: 'XCS:JTRK:REQ:I0' ipm: name: 'XCS-SB2-BMMON' diff --git a/jet_tracking/mpi_scripts/mpi_worker.py b/jet_tracking/mpi_scripts/mpi_worker.py index 48765a3..afa252e 100644 --- a/jet_tracking/mpi_scripts/mpi_worker.py +++ b/jet_tracking/mpi_scripts/mpi_worker.py @@ -113,7 +113,7 @@ def delta_bin(self, delta_bin): def start_run(self): """Worker should handle any calculations""" #mask_det = det.mask(188, unbond=True, unbondnbrs=True, status=True, edges=True, central=True) - ped = self.detector.pedestals(48)[0] + ped = self.detector.pedestals(218)[0] for evt_idx, evt in enumerate(self.ds.events()): if self.event_code not in self.evr.eventCodes(evt): continue From 8ec79257ec856961ede4a1caabb95b43af0ec9d0 Mon Sep 17 00:00:00 2001 From: Adam Date: Wed, 14 Apr 2021 14:48:28 -0700 Subject: [PATCH 14/23] runs through cal and produces results with MPIDataSource on ARP --- jet_tracking/jet_tracking_cal/jt_cal.py | 245 ++++++++++-------- .../jet_tracking_cal/submit_jt_cal_arp.sh | 4 +- jet_tracking/jt_configs/xcs_config.yml | 13 + 3 files changed, 147 insertions(+), 115 deletions(-) diff --git a/jet_tracking/jet_tracking_cal/jt_cal.py b/jet_tracking/jet_tracking_cal/jt_cal.py index 42cb5cb..bad3521 100644 --- a/jet_tracking/jet_tracking_cal/jt_cal.py +++ b/jet_tracking/jet_tracking_cal/jt_cal.py @@ -1,9 +1,7 @@ import h5py +from mpi4py import MPI import numpy as np -import matplotlib.pyplot as plt import logging -import re -import time import psana import yaml from scipy.optimize import curve_fit @@ -15,25 +13,16 @@ from bokeh.models import Span, Legend, LegendItem, ColorBar, LinearColorMapper from bokeh.io import output_notebook import panel as pn -from scipy.stats import gaussian_kde +# Need to go to stdout for arp/sbatch logger = logging.getLogger(__name__) +logger.setLevel(logging.DEBUG) +handler = logging.StreamHandler(sys.stdout) +handler.setLevel(logging.DEBUG) +logger.addHandler(handler) -# Constants -# Location of my branch for testing JT_LOC = '/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/' -# Number of bins -BINS = 100 -# Number of events to process -EVENTS = 1000 -# Percent of max in histogram to reject for I0 data -LR_THRESH = 0.1 -# Number of points at each end of azav to fit -LINE_FIT_POINTS = 5 -# Number of bins around peak to include in integrated intensity -DELTA_BIN = 5 - -# For now hold equations here since, will consolidate +SD_LOC = '/reg/data/ana15/' def get_r_masks(shape, bins=100): """Function to generate radial masks for pixels to include in azav""" @@ -84,7 +73,7 @@ def gaussian(x, a, mean, std, m, b): """ return (a * np.exp(-((x - mean) / 2 / std) ** 2)) + (m * x + b) -def fit_line(ave_azav, fit_points=LINE_FIT_POINTS): +def fit_line(ave_azav, fit_points=5): """ Fit the line from edges of array @@ -113,7 +102,7 @@ def fit_line(ave_azav, fit_points=LINE_FIT_POINTS): return m, b -def peak_lr(array_data, threshold=LR_THRESH, bins=BINS): +def peak_lr(array_data, threshold=0.1, bins=20): """Find max of normal distribution from histogram, search right and left until population falls below threshold, will run into problems with bimodal distribution. This is naive, @@ -197,7 +186,7 @@ def calc_azav_peak(ave_azav): return peak -def get_integrated_intensity(ave_azav, peak_bin, delta_bin=DELTA_BIN): +def get_integrated_intensity(ave_azav, peak_bin, delta_bin=3): """ Get the average integrated intensity. Sum the bin values from the peak bin to delta bin on each side. @@ -326,117 +315,147 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): if __name__ == '__main__': parser = ArgumentParser() - parser.add_argument('--exp', type=str, \ - default=(os.environ.get('EXPERIMENT', None))) - parser.add_argument('--run', type=str, \ - default=(os.environ.get('RUN_NUM', None))) parser.add_argument('--cfg', type=str, \ - default=(''.join([JT_LOC, 'mpi_scripts/mpi_configs/xcs_config.yml']))) - parser.add_argument('--delta_bin', type=int, \ - default=(DELTA_BIN)) - parser.add_argument('--bins', type=int, \ - default=(BINS)) + default=(''.join([JT_LOC, 'jt_configs/xcs_config.yml']))) args = parser.parse_args() + # Start spinning up processes + comm = MPI.COMM_WORLD + rank = comm.Get_rank() + size = comm.Get_size() + # All useful information should come from the config file # This will be source of truth for starting point for each hutch for now + # Can definitely be cleaned up/use environment variables for arp exp/run with open(args.cfg) as f: yml_dict = yaml.load(f, Loader=yaml.FullLoader) det_map = yml_dict['det_map'] ipm_name = yml_dict['ipm']['name'] ipm_det = yml_dict['ipm']['det'] + jet_cam_name = yml_dict['jet_cam']['name'] + jet_cam_axis = yml_dict['jet_cam']['axis'] hutch = yml_dict['hutch'] + exp = os.environ.get('EXPERIMENT', yml_dict['experiment']) + run = os.environ.get('RUN_NUM', yml_dict['run']) + cal_params = yml_dict['cal_params'] + + # Setup MPI data source + ds_name = ''.join(['exp=', exp, ':run=', run, ':smd']) + try: + ds = psana.MPIDataSource(ds_name) + except Exception as e: + logger.warning('Could not use MPI Data Source: {}'.format(e)) + sys.exit() - # Setup data source and write directories - exp_run = ''.join(['exp=', args.exp, ':run=', args.run]) - base_dir = ''.join(['/cds/data/psdm/', hutch, '/', args.exp, '/']) - exp_dir = ''.join([base_dir, 'xtc/']) - plots_dir = ''.join([base_dir, 'stats/summary/']) - results_dir = ''.join([base_dir, 'results']) - dsname = ''.join([exp_run, ':smd:', 'dir=', exp_dir]) - ds = psana.DataSource(dsname) + # Setup smd saver + jt_file = 'run{}_jt_cal.h5'.format(run) + jt_file_path = ''.join([SD_LOC, hutch, '/', exp, '/scratch/', jt_file]) + if rank == 0: + logger.info('Will save small data to {}'.format(jt_file_path)) + smd = ds.small_data(jt_file, gather_interval=100) # Get the detectors from the config - detector = psana.Detector(det_map['name']) - ipm = psana.Detector(ipm_name) - masks = get_r_masks(det_map['shape'], args.bins) - i0_data = [] - azav_data=[] - ped = detector.pedestals(int(args.run))[0] - logger.info('starting to evaluate 1000 events') - + try: + detector = psana.Detector(det_map['name']) + ipm = psana.Detector(ipm_name) + jet_cam = psana.Detector(jet_cam_name) + masks = get_r_masks(det_map['shape'], cal_params['azav_bins']) + except Exception as e: + logger.warning('Unable to create psana detectors: {}'.format(e)) + + if rank == 0: + logger.info('Gathering small data for exp: {}, run: {}, events: {}'.format(exp, run, cal_params['events'])) + logger.info('Detectors Available: {}'.format(psana.DetNames())) + + # Iterate through and pull out small data for evt_idx, evt in enumerate(ds.events()): - if evt_idx % 100 == 0: - logger.info('finished {} events'.format(evt_idx)) - print('finished {} events'.format(evt_idx)) - raw = detector.raw_data(evt) - ped - image = detector.image(evt, raw) - azav = np.array([np.mean(image[mask]) for mask in masks]) - azav_data.append(azav) try: - #i0_data.append(ipm.get(evt).f_12_ENRC()) - i0_data.append(getattr(ipm.get(evt), ipm_det)()) - except: - logger.warning('missing i0 for event {}'.format(evt_idx)) - i0_data.append(0.0) - - if evt_idx == 1000: + # Get image and azav + calib = detector.calib(evt) + det_image = detector.image(evt, calib) + azav = np.array([np.mean(det_image[mask]) for mask in masks]) + + # Get i0 Data + i0_data = getattr(ipm.get(evt), ipm_det)() + + # Get jet projection and location + jet_proj = jet_cam.image(evt).sum(axis=jet_cam_axis) + max_jet_val = np.amax(jet_proj) + max_jet_idx = np.where(max_jet_val == max_jet_val)[0] + smd.event(azav=azav, i0=i0_data, jet_peak=max_jet_val, jet_loc=max_jet_idx) + except Exception as e: + logger.info('Unable to process event {}: {}'.format(evt_idx, e)) + + if evt_idx == cal_params['events']: break - - # Find I0 distribution and filter out unused values - i0_data = np.array(i0_data) - i0_hist, i0_low, i0_high, i0_med = peak_lr(i0_data) - i0_idxs = np.where((i0_data > i0_low) & (i0_data < i0_high)) - i0_data_use = i0_data[i0_idxs] - # Generate figure for i0 params - p = peak_fig('i0 Values', i0_hist, i0_med, i0_low, i0_high) - - # Get the azav value we'll use - azav_use = [azav_data[idx] for idx in i0_idxs[0]] - ave_azav = np.array((np.sum(azav_use, axis=0)) / len(azav_use)) - # Find the peak bin from average azav values - peak_bin = calc_azav_peak(ave_azav) - - # Get the integrated intensity and generate fig - integrated_intensity = get_integrated_intensity(ave_azav, peak_bin, args.delta_bin) - p1 = azav_fig(ave_azav, peak_bin, integrated_intensity, args.delta_bin) - - # Go back through indices and find peak values for all the intensities - low_bin = peak_bin - args.delta_bin - high_bin = peak_bin + args.delta_bin - peak_vals = [azav[low_bin:high_bin].sum(axis=0) for azav in azav_use] - # Now fit I0 vs diffraction intensities - x, y, slope, intercept, sigma = fit_limits(i0_data_use, peak_vals, i0_low, i0_high) - p2 = intensity_vs_peak_fig(i0_data_use, peak_vals, x, y, slope, intercept, sigma) - - # Ratio information - ratios = peak_vals / i0_data_use - mean_ratio = np.mean(ratios) - med_ratio = np.median(ratios) - std_ratio = np.std(ratios) - - # Accumulate results - results = { - 'i0_low': i0_low, - 'i0_high': i0_high, - 'peak_bin': peak_bin, - 'delta_bin': args.delta_bin, - 'mean_ratio': mean_ratio, - 'med_ratio': med_ratio, - 'std_ratio': std_ratio - } - - print(' found results ', results) + + smd.save() + if rank == 0: + logger.info('Saved Small Data, Processing...') + while not os.path.exists(jt_file_path): + time.sleep(0.1) + + f = h5py.File(jt_file_path, 'r') + i0_data = np.array(f['i0']) + azav_data = np.array(f['azav']) + jet_loc = np.array(f['jet_loc']) + jet_peak = np.array(f['jet_peak']) + + # Find I0 distribution and filter out unused values + i0_data = np.array(i0_data) + i0_hist, i0_low, i0_high, i0_med = peak_lr(i0_data) + i0_idxs = np.where((i0_data > i0_low) & (i0_data < i0_high)) + i0_data_use = i0_data[i0_idxs] + + # Generate figure for i0 params + p = peak_fig('i0 Values', i0_hist, i0_med, i0_low, i0_high) + + # Get the azav value we'll use + azav_use = [azav_data[idx] for idx in i0_idxs[0]] + ave_azav = np.array((np.sum(azav_use, axis=0)) / len(azav_use)) + # Find the peak bin from average azav values + peak_bin = calc_azav_peak(ave_azav) + + # Get the integrated intensity and generate fig + integrated_intensity = get_integrated_intensity(ave_azav, peak_bin, cal_params['delta_bin']) + p1 = azav_fig(ave_azav, peak_bin, integrated_intensity, cal_params['delta_bin']) + + # Go back through indices and find peak values for all the intensities + low_bin = peak_bin - cal_params['delta_bin'] + high_bin = peak_bin + cal_params['delta_bin'] + peak_vals = [azav[low_bin:high_bin].sum(axis=0) for azav in azav_use] + # Now fit I0 vs diffraction intensities + x, y, slope, intercept, sigma = fit_limits(i0_data_use, peak_vals, i0_low, i0_high) + p2 = intensity_vs_peak_fig(i0_data_use, peak_vals, x, y, slope, intercept, sigma) + + # Ratio information + ratios = peak_vals / i0_data_use + mean_ratio = np.mean(ratios) + med_ratio = np.median(ratios) + std_ratio = np.std(ratios) + + # Accumulate results + results = { + 'i0_low': i0_low, + 'i0_high': i0_high, + 'peak_bin': peak_bin, + 'delta_bin': cal_params['delta_bin'], + 'mean_ratio': mean_ratio, + 'med_ratio': med_ratio, + 'std_ratio': std_ratio + } + + print(' found results ', results) # Write results to file - with open(''.join([results_dir, '/', args.run, '_results']), 'w') as f: - json.dumps(results, f, sort_keys=True, indent=4) + #with open(''.join([results_dir, '/', args.run, '_results']), 'w') as f: + # json.dumps(results, f, sort_keys=True, indent=4) # Accumulate plots and write - gspec = pn.GridSpec() - gspec[0:3, 0:3] = p - gspec[4:6, 0:3] = p1 - gspec[7:9, 0:3] = p2 - gspec.save(''.join([plots_dir, 'results_', args.run, '.html'])) + #gspec = pn.GridSpec() + #gspec[0:3, 0:3] = p + #gspec[4:6, 0:3] = p1 + #gspec[7:9, 0:3] = p2 + #gspec.save(''.join([plots_dir, 'results_', args.run, '.html'])) - print('finished with calibration') + print('finished with calibration') diff --git a/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh b/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh index 013ccc3..8ee1c5f 100755 --- a/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh +++ b/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh @@ -63,9 +63,9 @@ done set -- "${POSITIONAL[@]}" # Need to setup for FFB -QUEUE=${QUEUE:='psanaq'} +QUEUE=${QUEUE:='psfehhiprioq'} TASKS=${TASKS:=10} SCRIPT=${SCRIPT:=/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/jet_tracking_cal/jt_cal.py} CONFIG=${CONFIG:=/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/jt_configs/xcs_config.yml} -sbatch -p $QUEUE --ntasks $TASKS --wrap="mpirun python -u $SCRIPT $CONFIG" +sbatch -p $QUEUE --ntasks $TASKS --wrap="mpirun python -u $SCRIPT --cfg $CONFIG" diff --git a/jet_tracking/jt_configs/xcs_config.yml b/jet_tracking/jt_configs/xcs_config.yml index a963401..da1199e 100644 --- a/jet_tracking/jt_configs/xcs_config.yml +++ b/jet_tracking/jt_configs/xcs_config.yml @@ -3,6 +3,7 @@ api_msg: hutch: 'xcs' experiment: 'xcsx39718' +run: '10' det_map: name: 'epix10k2M' @@ -19,6 +20,18 @@ pv_map: ipm: name: 'XCS-SB2-BMMON' det: 'TotalIntensity' + +jet_cam: + name: 'opal_1' + axis: 0 + +cal_params: + azav_bins: 100 + events: 50 + i0_bins: 20 # Number of bins for i0 hist cuts + i0_reject: 0.1 # Percent below peak pin to make cut + fit_points: 5 # Number of points at start and end of azav array to do line fit + delta_bin: 3 # Number of azav bins around peak used for integration #ipm: # name: 'CXI-DG2-BMMON' # det: None From 2c3123276221a2a6c4e339cda51f681d586749e5 Mon Sep 17 00:00:00 2001 From: Adam Date: Fri, 16 Apr 2021 14:52:01 -0700 Subject: [PATCH 15/23] final jt cal state before I leave --- jet_tracking/jet_tracking_cal/jt_cal.py | 57 +++++++++++++------ .../jet_tracking_cal/submit_jt_cal_arp.sh | 3 +- jet_tracking/jt_configs/xcs_config.yml | 2 + 3 files changed, 45 insertions(+), 17 deletions(-) diff --git a/jet_tracking/jet_tracking_cal/jt_cal.py b/jet_tracking/jet_tracking_cal/jt_cal.py index bad3521..30939a2 100644 --- a/jet_tracking/jet_tracking_cal/jt_cal.py +++ b/jet_tracking/jet_tracking_cal/jt_cal.py @@ -13,6 +13,7 @@ from bokeh.models import Span, Legend, LegendItem, ColorBar, LinearColorMapper from bokeh.io import output_notebook import panel as pn +import matplotlib.pyplot as plt # Need to go to stdout for arp/sbatch logger = logging.getLogger(__name__) @@ -22,7 +23,7 @@ logger.addHandler(handler) JT_LOC = '/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/' -SD_LOC = '/reg/data/ana15/' +SD_LOC = '/reg/d/psdm/' def get_r_masks(shape, bins=100): """Function to generate radial masks for pixels to include in azav""" @@ -102,7 +103,7 @@ def fit_line(ave_azav, fit_points=5): return m, b -def peak_lr(array_data, threshold=0.1, bins=20): +def peak_lr(array_data, threshold=0.1, bins=50): """Find max of normal distribution from histogram, search right and left until population falls below threshold, will run into problems with bimodal distribution. This is naive, @@ -150,7 +151,7 @@ def peak_lr(array_data, threshold=0.1, bins=20): left = peak_idx - np.argmax(left_array[::-1] < threshold * peak_val) i0_low = edges[left] - return hist, i0_low, i0_high, i0_med + return hist, edges, i0_low, i0_high, i0_med def calc_azav_peak(ave_azav): """ @@ -237,7 +238,7 @@ def fit_limits(i0_data, peak_vals, i_low, i_high, bins=100): ###### Bokeh Figures ####### -def peak_fig(signal, hist, med, low, high): +def peak_fig(signal, hist, edges, med, low, high): """General histogram plotter with peak location and left/right limits plotted""" fig = figure( @@ -246,7 +247,7 @@ def peak_fig(signal, hist, med, low, high): x_axis_label='Intensity Values', y_axis_label='Counts' ) - fig.quad(top=hist, bottom=0, left=low, right=high) + fig.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:]) left_line = Span(location=low, dimension='height', \ line_color='black') right_line = Span(location=high, dimension='height', \ @@ -354,6 +355,9 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): logger.info('Will save small data to {}'.format(jt_file_path)) smd = ds.small_data(jt_file, gather_interval=100) + # Set report directory + results_dir = ''.join(['/reg/d/psdm/', hutch, '/', exp, '/stats/summary/JT_Cal_Run', run]) + # Get the detectors from the config try: detector = psana.Detector(det_map['name']) @@ -377,11 +381,13 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): # Get i0 Data i0_data = getattr(ipm.get(evt), ipm_det)() + if evt_idx == 5: + print('i0 data ', i0_data) # Get jet projection and location jet_proj = jet_cam.image(evt).sum(axis=jet_cam_axis) max_jet_val = np.amax(jet_proj) - max_jet_idx = np.where(max_jet_val == max_jet_val)[0] + max_jet_idx = np.where(max_jet_val==max_jet_val)[0] smd.event(azav=azav, i0=i0_data, jet_peak=max_jet_val, jet_loc=max_jet_idx) except Exception as e: logger.info('Unable to process event {}: {}'.format(evt_idx, e)) @@ -403,12 +409,19 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): # Find I0 distribution and filter out unused values i0_data = np.array(i0_data) - i0_hist, i0_low, i0_high, i0_med = peak_lr(i0_data) + i0_hist, edges, i0_low, i0_high, i0_med = peak_lr(i0_data) i0_idxs = np.where((i0_data > i0_low) & (i0_data < i0_high)) i0_data_use = i0_data[i0_idxs] - + + jet_loc_use = jet_loc[i0_idxs] + jet_loc_mean = np.mean(jet_loc_use) + jet_loc_std = np.std(jet_loc_use) + jet_peak_use = jet_peak[i0_idxs] + jet_peak_mean = np.mean(jet_peak_use) + jet_peak_std = np.std(jet_peak_use) + # Generate figure for i0 params - p = peak_fig('i0 Values', i0_hist, i0_med, i0_low, i0_high) + p = peak_fig('{}'.format(ipm_name), i0_hist, edges, i0_med, i0_low, i0_high) # Get the azav value we'll use azav_use = [azav_data[idx] for idx in i0_idxs[0]] @@ -438,24 +451,36 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): results = { 'i0_low': i0_low, 'i0_high': i0_high, + 'i0_median': i0_med, 'peak_bin': peak_bin, 'delta_bin': cal_params['delta_bin'], 'mean_ratio': mean_ratio, 'med_ratio': med_ratio, - 'std_ratio': std_ratio + 'std_ratio': std_ratio, + 'jet_location_mean': jet_loc_mean, + 'jet_location_std': jet_loc_std, + 'jet_peak_mean': jet_peak_mean, + 'jet_peak_std': jet_peak_std } - print(' found results ', results) + logger.info('Results: {}'.format(results)) # Write results to file #with open(''.join([results_dir, '/', args.run, '_results']), 'w') as f: # json.dumps(results, f, sort_keys=True, indent=4) # Accumulate plots and write - #gspec = pn.GridSpec() - #gspec[0:3, 0:3] = p - #gspec[4:6, 0:3] = p1 - #gspec[7:9, 0:3] = p2 - #gspec.save(''.join([plots_dir, 'results_', args.run, '.html'])) + gspec = pn.GridSpec(sizing_mode='stretch_both', name='JT Cal Results: Run {}'.format(run)) + gspec[0:3, 0:3] = p + gspec[4:6, 0:3] = p1 + gspec[7:12, 0:3] = p2 + tabs = pn.Tabs(gspec) + if not os.path.isdir(results_dir): + logger.info('Creating Path {}'.format(results_dir)) + os.makedirs(results_dir) + + results_file = ''.join([results_dir, '/report.html']) + logger.info('Saving results to {}'.format(results_file)) + tabs.save(results_file) print('finished with calibration') diff --git a/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh b/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh index 8ee1c5f..36f9879 100755 --- a/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh +++ b/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh @@ -21,7 +21,8 @@ EOF } -source /reg/g/psdm/etc/psconda.sh +source /reg/g/psdm/etc/psconda.sh -py3 +#conda activate ana-4.0.15-py3 # Use getopts when we get a chance POSITIONAL=() diff --git a/jet_tracking/jt_configs/xcs_config.yml b/jet_tracking/jt_configs/xcs_config.yml index da1199e..d1026f9 100644 --- a/jet_tracking/jt_configs/xcs_config.yml +++ b/jet_tracking/jt_configs/xcs_config.yml @@ -20,6 +20,8 @@ pv_map: ipm: name: 'XCS-SB2-BMMON' det: 'TotalIntensity' + #name: 'XCS-IPM-03' + #det: 'sum' jet_cam: name: 'opal_1' From f8b8d2f60ac969b7b34976ba401108c37cdfdd68 Mon Sep 17 00:00:00 2001 From: Adam Date: Tue, 20 Apr 2021 10:48:26 -0700 Subject: [PATCH 16/23] finish file saving, all to psana, give results via api call --- jet_tracking/jet_tracking_cal/jt_cal.py | 37 ++++++++++--------- .../jet_tracking_cal/submit_jt_cal_arp.sh | 4 +- jet_tracking/jt_configs/xcs_config.yml | 5 +-- 3 files changed, 23 insertions(+), 23 deletions(-) diff --git a/jet_tracking/jet_tracking_cal/jt_cal.py b/jet_tracking/jet_tracking_cal/jt_cal.py index 30939a2..23ca35a 100644 --- a/jet_tracking/jet_tracking_cal/jt_cal.py +++ b/jet_tracking/jet_tracking_cal/jt_cal.py @@ -340,6 +340,9 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): run = os.environ.get('RUN_NUM', yml_dict['run']) cal_params = yml_dict['cal_params'] + # Get Events for each worker + num_events = int(cal_params['events'] / size) + # Setup MPI data source ds_name = ''.join(['exp=', exp, ':run=', run, ':smd']) try: @@ -356,7 +359,7 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): smd = ds.small_data(jt_file, gather_interval=100) # Set report directory - results_dir = ''.join(['/reg/d/psdm/', hutch, '/', exp, '/stats/summary/JT_Cal_Run', run]) + results_dir = ''.join([SD_LOC, hutch, '/', exp, '/stats/summary/JT_Cal_Run', run]) # Get the detectors from the config try: @@ -379,20 +382,19 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): det_image = detector.image(evt, calib) azav = np.array([np.mean(det_image[mask]) for mask in masks]) - # Get i0 Data + # Get i0 Data this is different for differe ipm detectors + # Be nice not to waste cycles on getattr at some point i0_data = getattr(ipm.get(evt), ipm_det)() - if evt_idx == 5: - print('i0 data ', i0_data) # Get jet projection and location jet_proj = jet_cam.image(evt).sum(axis=jet_cam_axis) max_jet_val = np.amax(jet_proj) - max_jet_idx = np.where(max_jet_val==max_jet_val)[0] + max_jet_idx = np.where(jet_proj==max_jet_val)[0][0] smd.event(azav=azav, i0=i0_data, jet_peak=max_jet_val, jet_loc=max_jet_idx) except Exception as e: logger.info('Unable to process event {}: {}'.format(evt_idx, e)) - if evt_idx == cal_params['events']: + if evt_idx == num_events: break smd.save() @@ -465,22 +467,23 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): logger.info('Results: {}'.format(results)) - # Write results to file - #with open(''.join([results_dir, '/', args.run, '_results']), 'w') as f: - # json.dumps(results, f, sort_keys=True, indent=4) + if not os.path.isdir(results_dir): + logger.info('Creating Path {}'.format(results_dir)) + os.makedirs(results_dir) + + # Write metadata to file + with open(''.join([results_dir_dir, '/jt_cal_', run, '_results']), 'w') as f: + json.dumps(results, f, sort_keys=True, indent=4) - # Accumulate plots and write + # Accumulate plots and write report gspec = pn.GridSpec(sizing_mode='stretch_both', name='JT Cal Results: Run {}'.format(run)) gspec[0:3, 0:3] = p gspec[4:6, 0:3] = p1 gspec[7:12, 0:3] = p2 tabs = pn.Tabs(gspec) - if not os.path.isdir(results_dir): - logger.info('Creating Path {}'.format(results_dir)) - os.makedirs(results_dir) - results_file = ''.join([results_dir, '/report.html']) - logger.info('Saving results to {}'.format(results_file)) - tabs.save(results_file) + report_file = ''.join([results_dir, '/report.html']) + logger.info('Saving report to {}'.format(report_file)) + tabs.save(report_file) - print('finished with calibration') + logger.info('finished with jet tracking calibration') diff --git a/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh b/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh index 36f9879..73e76ba 100755 --- a/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh +++ b/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh @@ -64,9 +64,9 @@ done set -- "${POSITIONAL[@]}" # Need to setup for FFB -QUEUE=${QUEUE:='psfehhiprioq'} +QUEUE=${QUEUE:='psanaq'} TASKS=${TASKS:=10} SCRIPT=${SCRIPT:=/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/jet_tracking_cal/jt_cal.py} CONFIG=${CONFIG:=/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/jt_configs/xcs_config.yml} -sbatch -p $QUEUE --ntasks $TASKS --wrap="mpirun python -u $SCRIPT --cfg $CONFIG" +sbatch -p $QUEUE --ntasks $TASKS --job-name="jet track cal" --wrap="mpirun python -u $SCRIPT --cfg $CONFIG" diff --git a/jet_tracking/jt_configs/xcs_config.yml b/jet_tracking/jt_configs/xcs_config.yml index d1026f9..259adc8 100644 --- a/jet_tracking/jt_configs/xcs_config.yml +++ b/jet_tracking/jt_configs/xcs_config.yml @@ -29,11 +29,8 @@ jet_cam: cal_params: azav_bins: 100 - events: 50 + events: 500 i0_bins: 20 # Number of bins for i0 hist cuts i0_reject: 0.1 # Percent below peak pin to make cut fit_points: 5 # Number of points at start and end of azav array to do line fit delta_bin: 3 # Number of azav bins around peak used for integration -#ipm: -# name: 'CXI-DG2-BMMON' -# det: None From 195a788c109c8103457860644304318724f94d2d Mon Sep 17 00:00:00 2001 From: Adam Date: Tue, 20 Apr 2021 12:05:46 -0700 Subject: [PATCH 17/23] writing results in psana --- jet_tracking/jet_tracking_cal/jt_cal.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/jet_tracking/jet_tracking_cal/jt_cal.py b/jet_tracking/jet_tracking_cal/jt_cal.py index 23ca35a..008d457 100644 --- a/jet_tracking/jet_tracking_cal/jt_cal.py +++ b/jet_tracking/jet_tracking_cal/jt_cal.py @@ -472,8 +472,9 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): os.makedirs(results_dir) # Write metadata to file - with open(''.join([results_dir_dir, '/jt_cal_', run, '_results']), 'w') as f: - json.dumps(results, f, sort_keys=True, indent=4) + with open(''.join([results_dir, '/jt_cal_', run, '_results']), 'w') as f: + results = {k: str(v) for k, v in results.items()} + json.dump(results, f) # Accumulate plots and write report gspec = pn.GridSpec(sizing_mode='stretch_both', name='JT Cal Results: Run {}'.format(run)) From 2320869513564bac077166eff4ef0c6b66c8860c Mon Sep 17 00:00:00 2001 From: Adam Date: Thu, 22 Apr 2021 09:21:28 -0700 Subject: [PATCH 18/23] good stopping point before working on API --- jet_tracking/jet_tracking_cal/jt_cal.py | 16 +++- .../jet_tracking_cal/submit_jt_cal_arp.sh | 1 - jet_tracking/jt_configs/xcs_config.yml | 3 + jet_tracking/mpi_scripts/mpi_driver.py | 68 ++++++++++------ jet_tracking/mpi_scripts/mpi_master.py | 22 +++-- jet_tracking/mpi_scripts/mpi_worker.py | 66 ++++++++------- jet_tracking/mpi_scripts/runMpiScript | 81 ------------------- jet_tracking/mpi_scripts/run_mpi_script | 49 +++++++++++ 8 files changed, 152 insertions(+), 154 deletions(-) delete mode 100755 jet_tracking/mpi_scripts/runMpiScript create mode 100755 jet_tracking/mpi_scripts/run_mpi_script diff --git a/jet_tracking/jet_tracking_cal/jt_cal.py b/jet_tracking/jet_tracking_cal/jt_cal.py index 008d457..b0138b2 100644 --- a/jet_tracking/jet_tracking_cal/jt_cal.py +++ b/jet_tracking/jet_tracking_cal/jt_cal.py @@ -358,9 +358,6 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): logger.info('Will save small data to {}'.format(jt_file_path)) smd = ds.small_data(jt_file, gather_interval=100) - # Set report directory - results_dir = ''.join([SD_LOC, hutch, '/', exp, '/stats/summary/JT_Cal_Run', run]) - # Get the detectors from the config try: detector = psana.Detector(det_map['name']) @@ -369,6 +366,7 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): masks = get_r_masks(det_map['shape'], cal_params['azav_bins']) except Exception as e: logger.warning('Unable to create psana detectors: {}'.format(e)) + sys.exit() if rank == 0: logger.info('Gathering small data for exp: {}, run: {}, events: {}'.format(exp, run, cal_params['events'])) @@ -467,12 +465,22 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): logger.info('Results: {}'.format(results)) + # Set report directory + results_dir = ''.join([SD_LOC, hutch, '/', exp, '/stats/summary/jt_cal_run_', run]) + + # Get calib dir for meta data saving + calib_dir = ''.join([SD_LOC, hutch, '/', exp, '/calib/jt_results/']) + if not os.path.isdir(results_dir): logger.info('Creating Path {}'.format(results_dir)) os.makedirs(results_dir) + if not os.path.isdir(calib_dir): + logger.info('Creating Path {}'.format(calib_dir)) + os.makedirs(calib_dir) + # Write metadata to file - with open(''.join([results_dir, '/jt_cal_', run, '_results']), 'w') as f: + with open(''.join([calib_dir, '/jt_cal_', run, '_results']), 'w') as f: results = {k: str(v) for k, v in results.items()} json.dump(results, f) diff --git a/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh b/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh index 73e76ba..727404a 100755 --- a/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh +++ b/jet_tracking/jet_tracking_cal/submit_jt_cal_arp.sh @@ -22,7 +22,6 @@ EOF } source /reg/g/psdm/etc/psconda.sh -py3 -#conda activate ana-4.0.15-py3 # Use getopts when we get a chance POSITIONAL=() diff --git a/jet_tracking/jt_configs/xcs_config.yml b/jet_tracking/jt_configs/xcs_config.yml index 259adc8..de44d42 100644 --- a/jet_tracking/jt_configs/xcs_config.yml +++ b/jet_tracking/jt_configs/xcs_config.yml @@ -4,6 +4,7 @@ api_msg: hutch: 'xcs' experiment: 'xcsx39718' run: '10' +sim: true det_map: name: 'epix10k2M' @@ -16,6 +17,8 @@ det_map: pv_map: 1: 'XCS:JTRK:REQ:DIFF_INTENSITY' 2: 'XCS:JTRK:REQ:I0' + 3: 'XCS:JTRK:REQ:JET_PEAK' + 4: 'XCS:JTRK:REQ:JET_LOC' ipm: name: 'XCS-SB2-BMMON' diff --git a/jet_tracking/mpi_scripts/mpi_driver.py b/jet_tracking/mpi_scripts/mpi_driver.py index 90d171b..61b040a 100644 --- a/jet_tracking/mpi_scripts/mpi_driver.py +++ b/jet_tracking/mpi_scripts/mpi_driver.py @@ -1,4 +1,3 @@ -# Local imports from mpi_worker import MpiWorker from mpi_master import MpiMaster from utils import get_r_masks, get_evr_w_codes @@ -6,7 +5,13 @@ import psana import yaml import re +import json import argparse +import os +import sys +import logging + +logger = logging.getLogger(__name__) comm = MPI.COMM_WORLD size = comm.Get_size() @@ -14,46 +19,59 @@ # All the args parser = argparse.ArgumentParser() -parser.add_argument('--exprun', help='psana experiment/run string (e.g. exp=xppd7114:run=43)', type=str, default='') -#parser.add_argument('--dsname', help='data source name', type=str, default='') -parser.add_argument('--nevts', help='number of events', default=50, type=int) parser.add_argument('--cfg_file', help='if specified, has information about what metadata to use', type=str, default='xcs_config.yml') args = parser.parse_args() -# Two options for now, offline data or shared memory -if args.exprun: - info = re.split('=|:', args.exprun) - exp = info[1] - hutch = exp[:3] - exp_dir = ''.join(['/reg/d/psdm/', hutch, '/', exp, '/xtc/']) - dsname = ''.join([args.exprun, ':smd:', 'dir=', exp_dir]) -else: - dsname = 'shmem=psana.0:stop=no' - psana.setOption('psana.calib-dir', '/reg/d/psdm/xcs/xcsx39718/calib/') - # Parse config file to hand to workers -with open(''.join(['mpi_configs/', args.cfg_file])) as f: +with open(args.cfg_file) as f: yml_dict = yaml.load(f, Loader=yaml.FullLoader) api_port = yml_dict['api_msg']['port'] det_map = yml_dict['det_map'] ipm_name = yml_dict['ipm']['name'] ipm_det = yml_dict['ipm']['det'] pv_map = yml_dict['pv_map'] -print('here is pv map!!! ', pv_map) -# No way to do this only once with MPI + jet_cam_name = yml_dict['jet_cam']['name'] + jet_cam_axis = yml_dict['jet_cam']['axis'] + sim = yml_dict['sim'] + hutch = yml_dict['hutch'] + exp = yml_dict['experiment'] + run = yml_dict['run'] + +# Get calibration results +calib_dir = ''.join(['/cds/data/psdm/', hutch, '/', exp, '/calib/']) +jt_dir = ''.join([calib_dir, 'jt_results/']) + +cal_files = sorted(os.listdir(jt_dir)) +if cal_files: + cal_file = cal_files[-1] + cal_file_path = ''.join([jt_dir, cal_file]) + with open(cal_file_path) as f: + cal_results = json.load(f) +else: + logger.warning('You must run a calibration before starting jet tracking') + sys.exit() + +if sim: + # Run from offline data + exp_dir = ''.join(['/cds/data/psdm/', hutch, '/', exp, '/xtc/']) + dsname = ''.join(['exp=', exp, ':run=', run, ':smd:', 'dir=', exp_dir]) +else: + # Run on shared memeory + dsname = 'shmem=psana.0:stop=no' + psana.setOption('psana.calib-dir', calib_dir) + ds = psana.DataSource(dsname) -# Main detector we're looking at detector = psana.Detector(det_map['name']) -# Intensity monitor, could be wave8 or gdet with detector ipm = (psana.Detector(ipm_name), ipm_det) -# Because we never know hich evr will have event codes +jet_cam = psana.Detector(jet_cam_name) evr = get_evr_w_codes(psana.DetNames()) -# Get the R masks, would be great to do this only once r_mask = get_r_masks(det_map['shape']) -print(psana.DetNames()) + if rank == 0: - master = MpiMaster(rank, api_port, det_map, pv_map) + master = MpiMaster(rank, api_port, det_map, pv_map, sim=sim) master.start_run() else: - worker = MpiWorker(ds, args.nevts, detector, ipm, evr, r_mask) + peak_bin = int(cal_results['peak_bin']) + delta_bin = int(cal_results['delta_bin']) + worker = MpiWorker(ds, detector, ipm, jet_cam, jet_cam_axis, evr, r_mask, peak_bin=peak_bin, delta_bin=delta_bin) worker.start_run() diff --git a/jet_tracking/mpi_scripts/mpi_master.py b/jet_tracking/mpi_scripts/mpi_master.py index 10f8a39..d2650e5 100644 --- a/jet_tracking/mpi_scripts/mpi_master.py +++ b/jet_tracking/mpi_scripts/mpi_master.py @@ -15,11 +15,11 @@ class MpiMaster(object): - def __init__(self, rank, api_port, det_map, pv_map, psana=False, data_port=8123): + def __init__(self, rank, api_port, det_map, pv_map, sim=True, data_port=8123): self._rank = rank self._det_map = det_map self._pv_map = pv_map - self._psana = psana + self._sim = sim self._comm = MPI.COMM_WORLD self._workers = range(self._comm.Get_size())[1:] self._running = False @@ -72,7 +72,7 @@ def abort(self, val): def get_data_socket(self, data_port=8123): """Setup the socket we'll use for client data messaging""" - if self._psana: + if self._sim: context = zmq.Context() socket = context.socket(zmq.PUB) socket.bind(''.join(['tcp://*:', str(data_port)])) @@ -86,8 +86,7 @@ def start_run(self): """ while not self.abort: start = time.time() - # TODO: Generalize data length - data = np.empty(2, dtype=np.dtype(self.det_map['dtype'])) + data = np.empty(len(self._pv_map), dtype=np.dtype(self.det_map['dtype'])) req = self.comm.Irecv(data, source=MPI.ANY_SOURCE) self.send_from_queue() req.Wait() @@ -123,7 +122,7 @@ def start_msg_thread(self, api_port): def send_from_queue(self): if len(self.queue) > 0: data = self.queue.popleft() - if self._psana: + if self._sim: # Could need this if sending large arrays, # Could end up getting md info from config file md = dict( @@ -134,12 +133,9 @@ def send_from_queue(self): self._data_socket.send(data, 0, copy=False, track=False) else: # consider caput_many with lots, ok for now - #print('caputing data ', data) - #for k, v in self._pv_map: - #caput(v, data[k]) - #ratio = data[1] / data[0] - caput('XCS:JTRK:REQ:DIFF_INTENSITY', data[1]) - caput('XCS:JTRK:REQ:I0', data[0]) - #caput('CXI:JTRK:REQ:RATIO', ratio) + for k, v in self._pv_map.items(): + caput(v, data[k]) + #caput('XCS:JTRK:REQ:DIFF_INTENSITY', data[1]) + #caput('XCS:JTRK:REQ:I0', data[0]) else: pass diff --git a/jet_tracking/mpi_scripts/mpi_worker.py b/jet_tracking/mpi_scripts/mpi_worker.py index afa252e..5a678a4 100644 --- a/jet_tracking/mpi_scripts/mpi_worker.py +++ b/jet_tracking/mpi_scripts/mpi_worker.py @@ -22,17 +22,17 @@ class MpiWorker(object): """This worker will collect events and do whatever necessary processing, then send to master""" - def __init__(self, ds, evnt_lim, detector, ipm, evr, r_mask, latency=0.5, event_code=40, plot=False, peak_bin=25, delta_bin=5): + def __init__(self, ds, detector, ipm, jet_cam, jet_cam_axis, evr, r_mask, event_code=40, plot=False, peak_bin=25, delta_bin=5): self._ds = ds # We probably need to use kwargs to make this general - self._evnt_lim = evnt_lim self._detector = detector self._ipm = ipm + self._jet_cam = jet_cam + self._jet_cam_axis = jet_cam_axis self._evr = evr self._comm = MPI.COMM_WORLD self._rank = self._comm.Get_rank() self._r_mask = r_mask self._plot = plot - self._latency = latency self._event_code = event_code self._peak_bin = peak_bin self._delta_bin = delta_bin @@ -43,11 +43,6 @@ def rank(self): """Worker ID""" return self._rank - @property - def evnt_lim(self): - """Number of events for worker to process""" - return self._evnt_lim - @property def ds(self): """DataSource object""" @@ -78,11 +73,6 @@ def plot(self): """Whether we should plot detector""" return self._plot - @property - def latency(self): - """Max latency allowed between event and results""" - return self._latency - @property def event_code(self): """Event Code to trigger data collection on""" @@ -110,26 +100,42 @@ def delta_bin(self, delta_bin): except: logger.warning('You must provide int for delta bin') + @property + def jet_cam(self): + return self._jet_cam + + @property + def jet_cam_axis(self): + return self._jet_cam_axis + def start_run(self): """Worker should handle any calculations""" #mask_det = det.mask(188, unbond=True, unbondnbrs=True, status=True, edges=True, central=True) ped = self.detector.pedestals(218)[0] for evt_idx, evt in enumerate(self.ds.events()): - if self.event_code not in self.evr.eventCodes(evt): - continue - low_bin = self.peak_bin - self.delta_bin - hi_bin = self.peak_bin + self.delta_bin - raw = (self.detector.raw_data(evt) - ped) - data = self.detector.image(evt, raw) - az_bins = np.array([np.mean(data[mask]) for mask in self._r_mask[low_bin:hi_bin]]) - intensity = np.sum(az_bins) + # Definitely not a fan of wrapping the world in a try/except + # but too many possible failure modes from the data try: - i0 = self.ipm[0].get(evt) - if self.ipm[1]: - det = getattr(i0, self.ipm[1]) - i0 = det() - except: - i0 = 0.0 - - packet = np.array([i0, intensity], dtype='float32') - self.comm.Isend(packet, dest=0, tag=self.rank) + if self.event_code not in self.evr.eventCodes(evt): + continue + + low_bin = self.peak_bin - self.delta_bin + hi_bin = self.peak_bin + self.delta_bin + calib = self.detector.calib(evt) + det_image = self.detector.image(evt, calib) + az_bins = np.array([np.mean(det_image[mask]) for mask in self._r_mask[low_bin:hi_bin]]) + intensity = np.sum(az_bins) + + # Get i0 Data this is different for differe ipm detectors + i0 = getattr(self.ipm[0].get(evt), self.ipm[1])() + + # Get jet projection peak and location + jet_proj = self.jet_cam.image(evt).sum(axis=self.jet_cam_axis) + max_jet_val = np.amax(jet_proj) + max_jet_idx = np.where(jet_proj==max_jet_val)[0][0] + + packet = np.array([i0, intensity, max_jet_val, max_jet_idx], dtype='float32') + self.comm.Isend(packet, dest=0, tag=self.rank) + except Exception as e: + logger.warning('Unable to Process Event: {}'.format(e)) + continue diff --git a/jet_tracking/mpi_scripts/runMpiScript b/jet_tracking/mpi_scripts/runMpiScript deleted file mode 100755 index 9b82e14..0000000 --- a/jet_tracking/mpi_scripts/runMpiScript +++ /dev/null @@ -1,81 +0,0 @@ -#!/bin/bash - -usage() -{ -cat << EOF -$(basename "$0"): - Script to launch an mpirun - - OPTIONS: - -h|--help - Definition of options - -e|--exprun - Experiment and run name in format exp=xppd7114:run=43 - -d|--dsname - Data source name to gather events from - -n|--nevts - Number of events for each worker to process - -c|--cfgfile - Config file to load with damage/vars, and other things to parse for data aquisition - -p|--processors - Number of cores to use (available workers -1 for master) -EOF -} - -for arg in "$@" -do - case $arg in - -h|--help) - usage exit - ;; - -e|--exprun) - EXPRUN="$2" - shift - shift - ;; - -d|--dsname) - DSNAME="$2" - shift - shift - ;; - -n|--nevts) - NEVTS="$2" - shift - shift - ;; - -c|--cfgfile) - CFGFILE="$2" - shift - shift - ;; - -p|--processors) - PROC="$2" - shift - shift - ;; - esac -done - -# Pull out mpi_driver.py args -ARGS='' -if [[ -v EXPRUN ]]; then - ARGS+=' --exprun '$EXPRUN -fi -if [[ -v DSNAME ]]; then - ARGS+=' --dsname '$DSNAME -fi -if [[ -v NEVTS ]]; then - ARGS+=' --nevts '$NEVTS -fi -if [[ -v CFGFILE ]]; then - ARGS+=' --cfg_file '$CFGFILE -fi - -# If user doesn't specify use minimum required -PROC=${PROC:='2'} - -source /reg/g/pcds/setup/pathmunge.sh -source /reg/g/psdm/sw/conda1/manage/bin/psconda.sh -cd /cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/mpi_scripts -pythonpathmunge '/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking' -`which mpirun` -n $PROC python mpi_driver.py $ARGS diff --git a/jet_tracking/mpi_scripts/run_mpi_script b/jet_tracking/mpi_scripts/run_mpi_script new file mode 100755 index 0000000..2a776b8 --- /dev/null +++ b/jet_tracking/mpi_scripts/run_mpi_script @@ -0,0 +1,49 @@ +#!/bin/bash + +usage() +{ +cat << EOF +$(basename "$0"): + Script to launch an mpirun + + OPTIONS: + -h|--help + Definition of options + -c|--cfgfile + Config file to load with damage/vars, and other things to parse for data aquisition + -p|--processors + Number of cores to use (available workers -1 for master) +EOF +} + +for arg in "$@" +do + case $arg in + -h|--help) + usage exit + ;; + -c|--cfgfile) + CFGFILE="$2" + shift + shift + ;; + -p|--processors) + PROC="$2" + shift + shift + ;; + esac +done + +source /reg/g/psdm/etc/psconda.sh -py3 + +# If user doesn't specify use minimum required +PROC=${PROC:='2'} + +#source /reg/g/pcds/setup/pathmunge.sh +#source /reg/g/psdm/sw/conda1/manage/bin/psconda.sh +#cd /cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/mpi_scripts +#pythonpathmunge '/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking' +CONFIG=${CONFIG:=/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/jt_configs/xcs_config.yml} + +`which mpirun` -n $PROC python mpi_driver.py --cfg_file $CONFIG From 1e75ae8905ec393178495d2c3f7386eaabc9194b Mon Sep 17 00:00:00 2001 From: Adam Date: Thu, 22 Apr 2021 10:12:31 -0700 Subject: [PATCH 19/23] adding API calls --- jet_tracking/mpi_scripts/mpi_api.py | 13 ++++++++----- jet_tracking/mpi_scripts/mpi_master.py | 16 +++++++++++++--- 2 files changed, 21 insertions(+), 8 deletions(-) diff --git a/jet_tracking/mpi_scripts/mpi_api.py b/jet_tracking/mpi_scripts/mpi_api.py index 17ee959..beda047 100644 --- a/jet_tracking/mpi_scripts/mpi_api.py +++ b/jet_tracking/mpi_scripts/mpi_api.py @@ -3,10 +3,10 @@ import numpy as np import argparse parser = argparse.ArgumentParser() -parser.add_argument('--cfg_file', help='if specified, has information about what metadata to use', type=str, default='default_config.yml') +parser.add_argument('--cfg_file', help='if specified, has information about what metadata to use', type=str, default='xcs_config.yml') args = parser.parse_args() -with open(''.join(['mpi_configs/', args.cfg_file])) as f: +with open(''.join(['../jt_configs/', args.cfg_file])) as f: yml_dict = yaml.load(f, Loader=yaml.FullLoader) api_port = yml_dict['api_msg']['port'] @@ -28,8 +28,11 @@ def abort(): """Abort MPI run""" - socket.send('abort') + socket.send_pyobj({'cmd': 'abort', 'value': True}) -def pause(): +def set_peak_bin(peak_bin): """Pause MPI run""" - socket.send('pause') + socket.send_pyobj({'cmd': 'peak_bin', 'value': peak_bin}) + +def set_delta_bin(delta_bin): + socket.send_pyobj({'cmd': 'delta_bin', 'value': delta_bin}) diff --git a/jet_tracking/mpi_scripts/mpi_master.py b/jet_tracking/mpi_scripts/mpi_master.py index d2650e5..696962f 100644 --- a/jet_tracking/mpi_scripts/mpi_master.py +++ b/jet_tracking/mpi_scripts/mpi_master.py @@ -26,6 +26,7 @@ def __init__(self, rank, api_port, det_map, pv_map, sim=True, data_port=8123): self._abort = False self._queue = deque() self._data_socket = self.get_data_socket() + self._pub_socket = self.get_pub_socket() self._msg_thread = Thread(target=self.start_msg_thread, args=(api_port,)) self._msg_thread.start() @@ -80,6 +81,13 @@ def get_data_socket(self, data_port=8123): return None + def get_pub_socket(self, data_port=1234): + """Socket for publishing API calls to workers""" + context = zmq.Context() + socket = context.socket(zmq.PUB) + socket.bind(''.join(['tcp://*:', str(data_port)])) + return socket + def start_run(self): """Main process loop, we can probably get more async but for now it's a one to one recive/send @@ -112,9 +120,11 @@ def start_msg_thread(self, api_port): # TODO: make IP available arg socket.bind(''.join(['tcp://*:', str(api_port)])) while True: - message = socket.recv() - if message == 'abort': - self.abort = True + message = socket.recv_pyobj() + cmd = message['cmd'] + value = message['value'] + if cmd == 'abort': + self._pub_socket.send_pyobj(message) socket.send('aborted') else: print('Received Message with no definition ', message) From 46e16089bcb302b045c574d40bb60a6553f0be53 Mon Sep 17 00:00:00 2001 From: Adam Date: Thu, 22 Apr 2021 10:36:32 -0700 Subject: [PATCH 20/23] sim running ok on UI --- jet_tracking/datastream.py | 31 +++++++++++++------------- jet_tracking/mpi_scripts/mpi_master.py | 3 ++- 2 files changed, 18 insertions(+), 16 deletions(-) diff --git a/jet_tracking/datastream.py b/jet_tracking/datastream.py index 2599783..f435148 100644 --- a/jet_tracking/datastream.py +++ b/jet_tracking/datastream.py @@ -9,6 +9,7 @@ from PyQt5.QtGui import * from num_gen import sinwv import collections +import zmq logging = logging.getLogger('ophyd') logging.setLevel('CRITICAL') @@ -74,24 +75,24 @@ def live_data_stream(self): self.diff = self.signal_diff.get() def sim_data_stream(self): - """ + """Run with offline data""" context_data = zmq.Context() socket_data = context_data.socket(zmq.SUB) - socket_data.connect(".join(['tcp://localhost:', '8123'])") + socket_data.connect(''.join(['tcp://localhost:', '8123'])) socket_data.subscribe("") - while True: - md = socket_data.rev_json(flags=0) - msg = socket.recv(flags=0,copy=false, track=false) - buf = memoryview(msg) - data = np.frombuffer(buf, dtype=md['dtype']) - data = np.ndarray.tolist(data.reshape(md['shape'])) - self.gatt = data[0] - self.diff = data[1] - """ - x = 0.8 - y = 0.4 - self.gatt = sinwv(x) - self.diff = sinwv(y) + #while True: + md = socket_data.recv_json(flags=0) + msg = socket_data.recv(flags=0, copy=False, track=False) + buf = memoryview(msg) + data = np.frombuffer(buf, dtype=md['dtype']) + data = np.ndarray.tolist(data.reshape(md['shape'])) + self.gatt = data[0] + self.diff = data[1] + #time.sleep(0.1) + #x = 0.8 + #y = 0.4 + #self.gatt = sinwv(x) + #self.diff = sinwv(y) def read_value(self): # needs to initialize first maybe using a decorator? if self.live_data: diff --git a/jet_tracking/mpi_scripts/mpi_master.py b/jet_tracking/mpi_scripts/mpi_master.py index 696962f..07c49d1 100644 --- a/jet_tracking/mpi_scripts/mpi_master.py +++ b/jet_tracking/mpi_scripts/mpi_master.py @@ -125,7 +125,8 @@ def start_msg_thread(self, api_port): value = message['value'] if cmd == 'abort': self._pub_socket.send_pyobj(message) - socket.send('aborted') + socket.send(b'aborted') + print('received abort') else: print('Received Message with no definition ', message) From 23db9b56a7a6f540b4f2c0bbc928fdc13d9f4ac0 Mon Sep 17 00:00:00 2001 From: Adam Date: Fri, 23 Apr 2021 10:26:54 -0700 Subject: [PATCH 21/23] add basic api --- jet_tracking/datastream.py | 36 +++++++++++++++++-- jet_tracking/jet_tracking_cal/jt_cal.py | 5 +++ jet_tracking/jt_configs/xcs_config.yml | 2 +- jet_tracking/mpi_scripts/mpi_master.py | 47 +++++++++++++++---------- jet_tracking/mpi_scripts/mpi_worker.py | 38 +++++++++++++++++++- 5 files changed, 106 insertions(+), 22 deletions(-) diff --git a/jet_tracking/datastream.py b/jet_tracking/datastream.py index f435148..00a8468 100644 --- a/jet_tracking/datastream.py +++ b/jet_tracking/datastream.py @@ -10,12 +10,45 @@ from num_gen import sinwv import collections import zmq +import yaml logging = logging.getLogger('ophyd') logging.setLevel('CRITICAL') lock = threading.Lock() +# Constants +CFG_FILE = 'jt_configs/xcs_config.yml' + +def parse_config(cfg_file=CFG_FILE): + with open(args.cfg_file) as f: + yml_dict = yaml.load(f, Loader=yaml.FullLoader) + return yml_dict + #api_port = yml_dict['api_msg']['port'] + #det_map = yml_dict['det_map'] + #ipm_name = yml_dict['ipm']['name'] + #ipm_det = yml_dict['ipm']['det'] + #pv_map = yml_dict['pv_map'] + #jet_cam_name = yml_dict['jet_cam']['name'] + #jet_cam_axis = yml_dict['jet_cam']['axis'] + #sim = yml_dict['sim'] + #hutch = yml_dict['hutch'] + #exp = yml_dict['experiment'] + #run = yml_dict['run'] + +def get_cal_results(hutch, exp): + """This goes through the results directory and gets the lates one""" + results_dir = f'/cds/data/psdm/{hutch}/{exp}/calib/jt_results/' + cal_files = sorted(os.listdir(jt_dir)) + if cal_files: + cal_file = cal_files[-1] + cal_file_path = f'{results_dir}{cal_file}' + with open(cal_file_path) as f: + cal_results = json.load(f) + return cal_results + else: + return None + def GetPVs(): # this is where I would want to get PVs from a json file # but I will hard code it for now @@ -56,8 +89,7 @@ def __init__(self, signals): self.signals = signals self.PVs = dict() self.PV_signals = list() - self.live_data = True - + self.live_data = True self.signals.run_live.connect(self.run_live_data) def run_live_data(self, live): diff --git a/jet_tracking/jet_tracking_cal/jt_cal.py b/jet_tracking/jet_tracking_cal/jt_cal.py index b0138b2..a125ae4 100644 --- a/jet_tracking/jet_tracking_cal/jt_cal.py +++ b/jet_tracking/jet_tracking_cal/jt_cal.py @@ -385,6 +385,11 @@ def intensity_vs_peak_fig(intensity, peak_vals, x, y, slope, intercept, sigma): i0_data = getattr(ipm.get(evt), ipm_det)() # Get jet projection and location + if evt_idx == 5: + plt.imshow(jet_cam.image(evt)) + plt.show() + plt.plot(jet_cam.image(evt).sum(axis=jet_cam_axis)) + plt.show() jet_proj = jet_cam.image(evt).sum(axis=jet_cam_axis) max_jet_val = np.amax(jet_proj) max_jet_idx = np.where(jet_proj==max_jet_val)[0][0] diff --git a/jet_tracking/jt_configs/xcs_config.yml b/jet_tracking/jt_configs/xcs_config.yml index de44d42..2e05c05 100644 --- a/jet_tracking/jt_configs/xcs_config.yml +++ b/jet_tracking/jt_configs/xcs_config.yml @@ -28,7 +28,7 @@ ipm: jet_cam: name: 'opal_1' - axis: 0 + axis: 1 cal_params: azav_bins: 100 diff --git a/jet_tracking/mpi_scripts/mpi_master.py b/jet_tracking/mpi_scripts/mpi_master.py index 07c49d1..edabebc 100644 --- a/jet_tracking/mpi_scripts/mpi_master.py +++ b/jet_tracking/mpi_scripts/mpi_master.py @@ -5,7 +5,7 @@ import zmq import time from epics import caput -from threading import Thread +from threading import Thread, Lock from enum import Enum from collections import deque @@ -27,8 +27,11 @@ def __init__(self, rank, api_port, det_map, pv_map, sim=True, data_port=8123): self._queue = deque() self._data_socket = self.get_data_socket() self._pub_socket = self.get_pub_socket() + self._msg_lock = Lock() self._msg_thread = Thread(target=self.start_msg_thread, args=(api_port,)) self._msg_thread.start() + self.pair_ctx = None + self.msg_ctx = None @property def rank(self): @@ -69,22 +72,23 @@ def abort(self): def abort(self, val): """Set the abort flag""" if isinstance(val, bool): - self._abort = val + with self._msg_lock: + self._abort = val - def get_data_socket(self, data_port=8123): + def get_data_socket(self, data_port=8124): """Setup the socket we'll use for client data messaging""" if self._sim: - context = zmq.Context() - socket = context.socket(zmq.PUB) + self.msg_ctx = zmq.Context() + socket = self.msg_ctx.socket(zmq.PUB) socket.bind(''.join(['tcp://*:', str(data_port)])) return socket return None - def get_pub_socket(self, data_port=1234): + def get_pub_socket(self, data_port=1235): """Socket for publishing API calls to workers""" - context = zmq.Context() - socket = context.socket(zmq.PUB) + self.msg_ctx = zmq.Context() + socket = self.msg_ctx.socket(zmq.PUB) socket.bind(''.join(['tcp://*:', str(data_port)])) return socket @@ -100,14 +104,10 @@ def start_run(self): req.Wait() self.queue.append(data) print(time.time() - start) + self.pair_ctx.close() + self.msg_ctx.close() MPI.Finalize() -# status = MPI.Status() -# ready = self.comm.Iprobe(source=MPI.ANY_SOURCE, tag=MPI.ANY_TAG, status=status) -# if ready: -# data = np.empty(2, dtype=np.dtype(self.det_map['dtype'])) -# self.comm.Recv(data, source=status.Get_source(), tag=MPI.ANY_TAG, status=status) - def start_msg_thread(self, api_port): """The thread runs a PAIR communication and acts as server side, this allows for control of the parameters during data aquisition @@ -115,18 +115,29 @@ def start_msg_thread(self, api_port): we want messages to be handled by workers as well, or master can broadcast information """ - context = zmq.Context() - socket = context.socket(zmq.PAIR) + self.pair_ctx = zmq.Context() + socket = self.pair_ctx.socket(zmq.PAIR) # TODO: make IP available arg socket.bind(''.join(['tcp://*:', str(api_port)])) while True: message = socket.recv_pyobj() + print('got message ', message) cmd = message['cmd'] value = message['value'] if cmd == 'abort': self._pub_socket.send_pyobj(message) - socket.send(b'aborted') - print('received abort') + self.abort = True + logger.info('aborting jet tracking data analysis process') + elif cmd == 'peak_bin': + self._pub_socket.send_pyobj(message) + print('setting peak bin on master') + msg_string = 'Changing peak bin to {}'.format(value) + logger.info(msg_string) + elif cmd == 'delta_bin': + self._pub_socket.send_pyobj(message) + print('setting delta bin on master') + msg_string = 'Changing delta bin to {}'.format(value) + logger.info(msg_string) else: print('Received Message with no definition ', message) diff --git a/jet_tracking/mpi_scripts/mpi_worker.py b/jet_tracking/mpi_scripts/mpi_worker.py index 5a678a4..60d2354 100644 --- a/jet_tracking/mpi_scripts/mpi_worker.py +++ b/jet_tracking/mpi_scripts/mpi_worker.py @@ -12,6 +12,8 @@ import sys import time import inspect +from threading import Thread, Lock +import zmq from mpi4py import MPI f = '%(asctime)s - %(levelname)s - %(filename)s:%(funcName)s - %(message)s' @@ -22,7 +24,7 @@ class MpiWorker(object): """This worker will collect events and do whatever necessary processing, then send to master""" - def __init__(self, ds, detector, ipm, jet_cam, jet_cam_axis, evr, r_mask, event_code=40, plot=False, peak_bin=25, delta_bin=5): + def __init__(self, ds, detector, ipm, jet_cam, jet_cam_axis, evr, r_mask, event_code=40, plot=False, peak_bin=25, delta_bin=5, data_port=1235): self._ds = ds # We probably need to use kwargs to make this general self._detector = detector self._ipm = ipm @@ -37,6 +39,8 @@ def __init__(self, ds, detector, ipm, jet_cam, jet_cam_axis, evr, r_mask, event_ self._peak_bin = peak_bin self._delta_bin = delta_bin self._state = None + self._msg_thread = Thread(target=self.start_msg_thread, args=(data_port,)) + self._msg_thread.start() @property def rank(self): @@ -139,3 +143,35 @@ def start_run(self): except Exception as e: logger.warning('Unable to Process Event: {}'.format(e)) continue + + def start_msg_thread(self, data_port=1235): + """The thread runs a PAIR communication and acts as server side, + this allows for control of the parameters during data aquisition + from some client (probably an API for user). Might do subpub if + we want messages to be handled by workers as well, or master can + broadcast information + """ + context = zmq.Context() + socket = context.socket(zmq.SUB) + # TODO: make IP available arg + socket.connect(''.join(['tcp://localhost:', str(data_port)])) + socket.subscribe('') + print('running worker message thread') + while True: + message = socket.recv_pyobj() + cmd = message['cmd'] + value = message['value'] + print('worker got message ', message) + if cmd == 'abort': + self.abort = True + logger.info('aborting jet tracking data analysis process') + elif cmd == 'peak_bin': + print('got message peak bin ', value) + msg_string = 'Worker {} changing peak bin to {}'.format(self.rank, value) + logger.info(msg_string) + elif cmd == 'delta_bin': + msg_string = 'Worker {} changing delta bin to {}'.format(self.rank, value) + logger.info(msg_string) + else: + logger.warning('Worker {} received message with no definition {}'.format(self.rank, message)) + From 983c2dd6133895ce10362499fbc76277305a1c92 Mon Sep 17 00:00:00 2001 From: Adam Date: Fri, 23 Apr 2021 10:28:00 -0700 Subject: [PATCH 22/23] start of readme --- README.md | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..0c747a5 --- /dev/null +++ b/README.md @@ -0,0 +1,45 @@ +#Jet Tracking Application +The purpose of this application is to automate the positioning of the liquid jet to be conincident with the x-rays. This version is a start and mostly a proof of concept, because everyone knows you don't build something right the first time ever. Once this is fully functional then it can be rebuilt with a better architecture and file structure using the proven pieces. + +##Calibration +The calibration piece is used to identify the typical diffraction ring intensity from the solvent/substrate present in the liquid jet. The current procedure is to take about 10 seconds of data in a recorded run then analyze the following: +- Making a cut on the distribution of incoming x ray intensity to identify events with good x ray intensity +- Get the azimuthal average of the area detector for all of those events and identifying the peak intensity (brightest bin of the ring). Then summing the intensities of the peak bin and a +/- delta bin value. +- Get the projection of the jet camera and identify the peak intensity and location of that jet. + +###How to run the calibration +There are two ways to run the calibration. +The suggested/production way is to run through Automatic Run Processing on pswww. +There is a current definition and run setup for xcsx39718 on Run 82. You can see the results in the summaries tab for that experiment (elog (aka Data Manager) on pswww) + +All of the meta data information is then saved in a json file with the path: +/cds/data/psdm///calib/jt_results + +The second way to run the calibration is to do it locally, this is much easier for development. In order to simplify and organize meta data as input parameters for the calibration we use config files located at /jet_tracking/jt_configs. You need to change information there is you want to adjust certain calibration parameters. to run you must be on a psana node + +``` +$ ssh psana +$ cd /jet_tracking/jet_tracking/jet_tracking_cal +$ source /reg/g/psdm/etc/psconda.sh -py3 +$ python jt_cal.py --cfg # The default is xcs_config.yml so no arg required if using that one +``` + +Sample Output +``` +(ana-4.0.20-py3) aegger@psanagpu112:/cds/group/pcds/epics-dev/aegger/jet_tracking/jet_tracking/jet_tracking_cal$ python jt_cal.py +Will save small data to /reg/d/psdm/xcs/xcsx39718/scratch/run10_jt_cal.h5 +Gathering small data for exp: xcsx39718, run: 10, events: 500 +Detectors Available: [('XcsEndstation.1:ControlsCamera.16', 'xcs_yag4', ''), ('EBeam', '', ''), ('FEEGasDetEnergy', '', ''), ('XCS-IPM-01', '', ''), ('XCS-IPM-03', '', ''), ('XCS-DIO-03', '', ''), ('HX2-SB1-BMMON', '', ''), ('XCS-SB1-BMMON', '', ''), ('XCS-SB2-BMMON', '', ''), ('XcsEndstation.0:Epix10ka.1', 'epix10k135', ''), ('NoDetector.0:Evr.0', 'evr0', ''), ('XcsEndstation.0:Epix10ka2M.0', 'epix10k2M', ''), ('XcsEndstation.1:Opal1000.1', 'opal_1', ''), ('ControlData', '', '')] +Unable to process event 0: 'NoneType' object has no attribute 'TotalIntensity' +Saved Small Data, Processing... +Results: {'i0_low': 53345.170000000006, 'i0_high': 93364.9225, 'i0_median': 74307.8975, 'peak_bin': 12, 'delta_bin': 3, 'mean_ratio': 0.1453248744739173, 'med_ratio': 0.1463255684260074, 'std_ratio': 0.03161866013604559, 'jet_location_mean': 0.0, 'jet_location_std': 0.0, 'jet_peak_mean': 30354.924, 'jet_peak_std': 326.71924} +Creating Path /reg/d/psdm/xcs/xcsx39718/stats/summary/jt_cal_run_10 +Saving report to /reg/d/psdm/xcs/xcsx39718/stats/summary/jt_cal_run_10/report.html +finished with jet tracking calibration +Closing remaining open files:run10_jt_cal.h5...done +``` +## Running the shared memory process +Once we have the needed calibration data, you can run the shared memory process + + + From 1f8d64e6fd16a312bea8ccde88e5bd179fd316cc Mon Sep 17 00:00:00 2001 From: Adam Date: Fri, 23 Apr 2021 11:02:36 -0700 Subject: [PATCH 23/23] final commit while working here --- README.md | 16 ++++++++++++++- jet_tracking/mpi_scripts/mpi_master.py | 3 --- jet_tracking/mpi_scripts/mpi_worker.py | 28 +++++++++++++++----------- 3 files changed, 31 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 0c747a5..08e1e5d 100644 --- a/README.md +++ b/README.md @@ -38,8 +38,22 @@ Saving report to /reg/d/psdm/xcs/xcsx39718/stats/summary/jt_cal_run_10/report.ht finished with jet tracking calibration Closing remaining open files:run10_jt_cal.h5...done ``` -## Running the shared memory process +##Running the shared memory process Once we have the needed calibration data, you can run the shared memory process +###Sim Mode +If you set the sim variable to true in the config file, you will run in sim mode. This means you will read offline data. This is only setup to use one worker and a master so it's somewhat slow, but very good for debugging. +``` +$ ssh psana +$ cd /jet_tracking/jet_tracking/mpi_scripts +$ ./run_mpi_script +``` +###Shared Memory +To run in shared memory you need to ssh to the mon node that has shared memory running. +``` +$ ssh daq-cxi-mon01 +$ cd /jet_tracking/jet_tracking/mpi_scripts +$ ./run_mpi_script -p 8 # -p tells number of cores to use 1 Master, the reset workers +``` diff --git a/jet_tracking/mpi_scripts/mpi_master.py b/jet_tracking/mpi_scripts/mpi_master.py index edabebc..b84070b 100644 --- a/jet_tracking/mpi_scripts/mpi_master.py +++ b/jet_tracking/mpi_scripts/mpi_master.py @@ -121,7 +121,6 @@ def start_msg_thread(self, api_port): socket.bind(''.join(['tcp://*:', str(api_port)])) while True: message = socket.recv_pyobj() - print('got message ', message) cmd = message['cmd'] value = message['value'] if cmd == 'abort': @@ -130,12 +129,10 @@ def start_msg_thread(self, api_port): logger.info('aborting jet tracking data analysis process') elif cmd == 'peak_bin': self._pub_socket.send_pyobj(message) - print('setting peak bin on master') msg_string = 'Changing peak bin to {}'.format(value) logger.info(msg_string) elif cmd == 'delta_bin': self._pub_socket.send_pyobj(message) - print('setting delta bin on master') msg_string = 'Changing delta bin to {}'.format(value) logger.info(msg_string) else: diff --git a/jet_tracking/mpi_scripts/mpi_worker.py b/jet_tracking/mpi_scripts/mpi_worker.py index 60d2354..c9f15e3 100644 --- a/jet_tracking/mpi_scripts/mpi_worker.py +++ b/jet_tracking/mpi_scripts/mpi_worker.py @@ -41,6 +41,7 @@ def __init__(self, ds, detector, ipm, jet_cam, jet_cam_axis, evr, r_mask, event_ self._state = None self._msg_thread = Thread(target=self.start_msg_thread, args=(data_port,)) self._msg_thread.start() + self._attr_lock = Lock() @property def rank(self): @@ -88,10 +89,11 @@ def peak_bin(self): @peak_bin.setter def peak_bin(self, peak_bin): - try: - self._peak_bin = int(peak_bin) - except: - logger.warning('You must provide int for peak bin') + with self._attr_lock: + try: + self._peak_bin = int(peak_bin) + except: + logger.warning('You must provide int for peak bin') @property def delta_bin(self): @@ -99,10 +101,11 @@ def delta_bin(self): @delta_bin.setter def delta_bin(self, delta_bin): - try: - self._delta_bin = int(delta_bin) - except: - logger.warning('You must provide int for delta bin') + with self._attr_lock: + try: + self._delta_bin = int(delta_bin) + except: + logger.warning('You must provide int for delta bin') @property def jet_cam(self): @@ -123,8 +126,9 @@ def start_run(self): if self.event_code not in self.evr.eventCodes(evt): continue - low_bin = self.peak_bin - self.delta_bin - hi_bin = self.peak_bin + self.delta_bin + with self._attr_lock: + low_bin = self.peak_bin - self.delta_bin + hi_bin = self.peak_bin + self.delta_bin calib = self.detector.calib(evt) det_image = self.detector.image(evt, calib) az_bins = np.array([np.mean(det_image[mask]) for mask in self._r_mask[low_bin:hi_bin]]) @@ -161,17 +165,17 @@ def start_msg_thread(self, data_port=1235): message = socket.recv_pyobj() cmd = message['cmd'] value = message['value'] - print('worker got message ', message) if cmd == 'abort': self.abort = True logger.info('aborting jet tracking data analysis process') elif cmd == 'peak_bin': - print('got message peak bin ', value) msg_string = 'Worker {} changing peak bin to {}'.format(self.rank, value) logger.info(msg_string) + self.peak_bin = int(value) elif cmd == 'delta_bin': msg_string = 'Worker {} changing delta bin to {}'.format(self.rank, value) logger.info(msg_string) + self.delta_bin = int(value) else: logger.warning('Worker {} received message with no definition {}'.format(self.rank, message))